diff --git a/README b/README index 34a28f1..0034999 100644 --- a/README +++ b/README @@ -1,14 +1,23 @@ GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction -(C) 2007-2010, David A. Bader - Amrita Mathuriya +(C) 2007-2011, David A. Bader College of Computing, Georgia Institute of Technology Christine E. Heitsch School of Mathematics, Georgia Institute of Technology Stephen C. Harvey School of Biology, Georgia Institute of Technology - Sainath Mallidi - College of Computing, Georgia Institute of Technology + And various contributing authors + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program. If not, see . The prediction of the correct secondary structures of large RNAs is one of the unsolved challenges of computational molecular biology. @@ -28,8 +37,11 @@ DBI-04-20513. Additionally, the research of Christine E. Heitsch, Ph.D., is supported in part by a Career Award at the Scientific Interface (CASI) from the Burroughs Wellcome Fund (BWF). -Additional contributors to GTfold's implementation include Georgia -Tech visiting students Gregory Nou, Sonny Hernandez, and Manoj Soni. +Additional contributors to GTfold's implementation include +Georgia Tech graduate students Sainath Mallidi, Amrita Mathuriya, +and Prashant Gaurav, undergraduates Joshua Anderson and Andrew Ash +and visiting students Gregory Nou, Sonny Hernandez, Manoj Soni, +and Zsuzsanna Sukosd. INSTALLATION - Please execute the following commands @@ -110,4 +122,18 @@ Version History: 1.16 20 May 2010 Fixed another nasty bug with prohibited constraints handling. Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure. Some documentation added. - +2.0 11 July 2011 + Optimized the code to enable faster multiloop calculations + Added -d, --dangle to allow treatment of dangling end energies based on user input + Added -m --mismatch to enable terminal mismatch calculations + Added -o, --output, , -w --workdir options to allow to write output files/directories with desired name + Added -p --paramdir to allow user to provide custom parameters + Added -t, --threads to limit number of threads used + Added -v, --verbose to print loop-by-loop energy decomposition and confirm that constraints are satisfied + Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides + such that it could be part of a helix of length INT + Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) + Added --unafold to run GTfold in UNAfold default mode (version 3.8) + Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE + Added --bpp (Beta only) which outputs basepair probabilities based on the partition function + Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data diff --git a/gtfold-mfe/AUTHORS b/gtfold-mfe/AUTHORS index 0f01d3b..0e9ed76 100644 --- a/gtfold-mfe/AUTHORS +++ b/gtfold-mfe/AUTHORS @@ -4,4 +4,5 @@ Amrita Mathuriya August 2007 - January 2009 Sainath Mallidi August 2009 - December 2010 Josh Anderson August 2010 - May 2011 Andrew Ash August 2010 - May 2011 +Zsuzsanna Sukosd February 2011 - June 2011 Prashant Gaurav August 2010 - diff --git a/gtfold-mfe/INSTALL b/gtfold-mfe/INSTALL index 54caf7c..7d1c323 100644 --- a/gtfold-mfe/INSTALL +++ b/gtfold-mfe/INSTALL @@ -1,13 +1,25 @@ -Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002 Free Software -Foundation, Inc. +Installation Instructions +************************* - This file is free documentation; the Free Software Foundation gives -unlimited permission to copy, distribute and modify it. +Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005, +2006, 2007, 2008, 2009 Free Software Foundation, Inc. + + Copying and distribution of this file, with or without modification, +are permitted in any medium without royalty provided the copyright +notice and this notice are preserved. This file is offered as-is, +without warranty of any kind. Basic Installation ================== - These are generic installation instructions. + Briefly, the shell commands `./configure; make; make install' should +configure, build, and install this package. The following +more-detailed instructions are generic; see the `README' file for +instructions specific to this package. Some packages provide this +`INSTALL' file but do not implement all of the features documented +below. The lack of an optional feature in a given package is not +necessarily a bug. More recommendations for GNU packages can be found +in *note Makefile Conventions: (standards)Makefile Conventions. The `configure' shell script attempts to guess correct values for various system-dependent variables used during compilation. It uses @@ -20,9 +32,9 @@ debugging `configure'). It can also use an optional file (typically called `config.cache' and enabled with `--cache-file=config.cache' or simply `-C') that saves -the results of its tests to speed up reconfiguring. (Caching is +the results of its tests to speed up reconfiguring. Caching is disabled by default to prevent problems with accidental use of stale -cache files.) +cache files. If you need to do unusual things to compile the package, please try to figure out how `configure' could check whether to do them, and mail @@ -32,30 +44,37 @@ some point `config.cache' contains results you don't want to keep, you may remove or edit it. The file `configure.ac' (or `configure.in') is used to create -`configure' by a program called `autoconf'. You only need -`configure.ac' if you want to change it or regenerate `configure' using -a newer version of `autoconf'. +`configure' by a program called `autoconf'. You need `configure.ac' if +you want to change it or regenerate `configure' using a newer version +of `autoconf'. -The simplest way to compile this package is: + The simplest way to compile this package is: 1. `cd' to the directory containing the package's source code and type - `./configure' to configure the package for your system. If you're - using `csh' on an old version of System V, you might need to type - `sh ./configure' instead to prevent `csh' from trying to execute - `configure' itself. + `./configure' to configure the package for your system. - Running `configure' takes awhile. While running, it prints some - messages telling which features it is checking for. + Running `configure' might take a while. While running, it prints + some messages telling which features it is checking for. 2. Type `make' to compile the package. 3. Optionally, type `make check' to run any self-tests that come with - the package. + the package, generally using the just-built uninstalled binaries. 4. Type `make install' to install the programs and any data files and - documentation. - - 5. You can remove the program binaries and object files from the + documentation. When installing into a prefix owned by root, it is + recommended that the package be configured and built as a regular + user, and only the `make install' phase executed with root + privileges. + + 5. Optionally, type `make installcheck' to repeat any self-tests, but + this time using the binaries in their final installed location. + This target does not install anything. Running this target as a + regular user, particularly if the prior `make install' required + root privileges, verifies that the installation completed + correctly. + + 6. You can remove the program binaries and object files from the source code directory by typing `make clean'. To also remove the files that `configure' created (so you can compile the package for a different kind of computer), type `make distclean'. There is @@ -64,6 +83,16 @@ The simplest way to compile this package is: all sorts of other programs in order to regenerate files that came with the distribution. + 7. Often, you can also type `make uninstall' to remove the installed + files again. In practice, not all packages have tested that + uninstallation works correctly, even though it is required by the + GNU Coding Standards. + + 8. Some packages, particularly those that use Automake, provide `make + distcheck', which can by used by developers to test that all other + targets like `make install' and `make uninstall' work correctly. + This target is generally not run by end users. + Compilers and Options ===================== @@ -75,7 +104,7 @@ for details on some of the pertinent environment variables. by setting variables in the command line or in the environment. Here is an example: - ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix + ./configure CC=c99 CFLAGS=-g LIBS=-lposix *Note Defining Variables::, for more details. @@ -84,44 +113,89 @@ Compiling For Multiple Architectures You can compile the package for more than one kind of computer at the same time, by placing the object files for each architecture in their -own directory. To do this, you must use a version of `make' that -supports the `VPATH' variable, such as GNU `make'. `cd' to the +own directory. To do this, you can use GNU `make'. `cd' to the directory where you want the object files and executables to go and run the `configure' script. `configure' automatically checks for the -source code in the directory that `configure' is in and in `..'. +source code in the directory that `configure' is in and in `..'. This +is known as a "VPATH" build. - If you have to use a `make' that does not support the `VPATH' -variable, you have to compile the package for one architecture at a -time in the source code directory. After you have installed the -package for one architecture, use `make distclean' before reconfiguring -for another architecture. + With a non-GNU `make', it is safer to compile the package for one +architecture at a time in the source code directory. After you have +installed the package for one architecture, use `make distclean' before +reconfiguring for another architecture. + + On MacOS X 10.5 and later systems, you can create libraries and +executables that work on multiple system types--known as "fat" or +"universal" binaries--by specifying multiple `-arch' options to the +compiler but only a single `-arch' option to the preprocessor. Like +this: + + ./configure CC="gcc -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ + CXX="g++ -arch i386 -arch x86_64 -arch ppc -arch ppc64" \ + CPP="gcc -E" CXXCPP="g++ -E" + + This is not guaranteed to produce working output in all cases, you +may have to build one architecture at a time and combine the results +using the `lipo' tool if you have problems. Installation Names ================== - By default, `make install' will install the package's files in -`/usr/local/bin', `/usr/local/man', etc. You can specify an -installation prefix other than `/usr/local' by giving `configure' the -option `--prefix=PATH'. + By default, `make install' installs the package's commands under +`/usr/local/bin', include files under `/usr/local/include', etc. You +can specify an installation prefix other than `/usr/local' by giving +`configure' the option `--prefix=PREFIX', where PREFIX must be an +absolute file name. You can specify separate installation prefixes for architecture-specific files and architecture-independent files. If you -give `configure' the option `--exec-prefix=PATH', the package will use -PATH as the prefix for installing programs and libraries. -Documentation and other data files will still use the regular prefix. +pass the option `--exec-prefix=PREFIX' to `configure', the package uses +PREFIX as the prefix for installing programs and libraries. +Documentation and other data files still use the regular prefix. In addition, if you use an unusual directory layout you can give -options like `--bindir=PATH' to specify different values for particular +options like `--bindir=DIR' to specify different values for particular kinds of files. Run `configure --help' for a list of the directories -you can set and what kinds of files go in them. +you can set and what kinds of files go in them. In general, the +default for these options is expressed in terms of `${prefix}', so that +specifying just `--prefix' will affect all of the other directory +specifications that were not explicitly provided. + + The most portable way to affect installation locations is to pass the +correct locations to `configure'; however, many packages provide one or +both of the following shortcuts of passing variable assignments to the +`make install' command line to change installation locations without +having to reconfigure or recompile. + + The first method involves providing an override variable for each +affected directory. For example, `make install +prefix=/alternate/directory' will choose an alternate location for all +directory configuration variables that were expressed in terms of +`${prefix}'. Any directories that were specified during `configure', +but not in terms of `${prefix}', must each be overridden at install +time for the entire installation to be relocated. The approach of +makefile variable overrides for each directory variable is required by +the GNU Coding Standards, and ideally causes no recompilation. +However, some platforms have known limitations with the semantics of +shared libraries that end up requiring recompilation when using this +method, particularly noticeable in packages that use GNU Libtool. + + The second method involves providing the `DESTDIR' variable. For +example, `make install DESTDIR=/alternate/directory' will prepend +`/alternate/directory' before all installation names. The approach of +`DESTDIR' overrides is not required by the GNU Coding Standards, and +does not work on platforms that have drive letters. On the other hand, +it does better at avoiding recompilation issues, and works well even +when some directory options were not specified in terms of `${prefix}' +at `configure' time. + +Optional Features +================= If the package supports it, you can cause programs to be installed with an extra prefix or suffix on their names by giving `configure' the option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'. -Optional Features -================= - Some packages pay attention to `--enable-FEATURE' options to `configure', where FEATURE indicates an optional part of the package. They may also pay attention to `--with-PACKAGE' options, where PACKAGE @@ -134,6 +208,45 @@ find the X include and library files automatically, but if it doesn't, you can use the `configure' options `--x-includes=DIR' and `--x-libraries=DIR' to specify their locations. + Some packages offer the ability to configure how verbose the +execution of `make' will be. For these packages, running `./configure +--enable-silent-rules' sets the default to minimal output, which can be +overridden with `make V=1'; while running `./configure +--disable-silent-rules' sets the default to verbose, which can be +overridden with `make V=0'. + +Particular systems +================== + + On HP-UX, the default C compiler is not ANSI C compatible. If GNU +CC is not installed, it is recommended to use the following options in +order to use an ANSI C compiler: + + ./configure CC="cc -Ae -D_XOPEN_SOURCE=500" + +and if that doesn't work, install pre-built binaries of GCC for HP-UX. + + On OSF/1 a.k.a. Tru64, some versions of the default C compiler cannot +parse its `' header file. The option `-nodtk' can be used as +a workaround. If GNU CC is not installed, it is therefore recommended +to try + + ./configure CC="cc" + +and if that doesn't work, try + + ./configure CC="cc -nodtk" + + On Solaris, don't put `/usr/ucb' early in your `PATH'. This +directory contains several dysfunctional programs; working variants of +these programs are available in `/usr/bin'. So, if you need `/usr/ucb' +in your `PATH', put it _after_ `/usr/bin'. + + On Haiku, software installed for all users goes in `/boot/common', +not `/usr/local'. It is recommended to use the following options: + + ./configure --prefix=/boot/common + Specifying the System Type ========================== @@ -149,14 +262,15 @@ type, such as `sun4', or a canonical name which has the form: where SYSTEM can have one of these forms: - OS KERNEL-OS + OS + KERNEL-OS See the file `config.sub' for the possible values of each field. If `config.sub' isn't included in this package, then this package doesn't need to know the machine type. If you are _building_ compiler tools for cross-compiling, you should -use the `--target=TYPE' option to select the type of system they will +use the option `--target=TYPE' to select the type of system they will produce code for. If you want to _use_ a cross compiler, that generates code for a @@ -186,9 +300,14 @@ them in the `configure' command line, using `VAR=value'. For example: ./configure CC=/usr/local2/bin/gcc -will cause the specified gcc to be used as the C compiler (unless it is +causes the specified `gcc' to be used as the C compiler (unless it is overridden in the site shell script). +Unfortunately, this technique does not work for `CONFIG_SHELL' due to +an Autoconf bug. Until the bug is fixed you can use this workaround: + + CONFIG_SHELL=/bin/bash /bin/bash ./configure CONFIG_SHELL=/bin/bash + `configure' Invocation ====================== @@ -197,7 +316,14 @@ operates. `--help' `-h' - Print a summary of the options to `configure', and exit. + Print a summary of all of the options to `configure', and exit. + +`--help=short' +`--help=recursive' + Print a summary of the options unique to this package's + `configure', and exit. The `short' variant lists options used + only in the top level, while the `recursive' variant lists options + also present in any nested packages. `--version' `-V' @@ -224,6 +350,16 @@ operates. Look for the package's source code in directory DIR. Usually `configure' can determine that directory automatically. +`--prefix=DIR' + Use DIR as the installation prefix. *note Installation Names:: + for more details, including other options available for fine-tuning + the installation locations. + +`--no-create' +`-n' + Run the configure checks, but stop before creating any output + files. + `configure' also accepts some other, not widely useful, options. Run `configure --help' for more details. diff --git a/gtfold-mfe/Makefile.in b/gtfold-mfe/Makefile.in index 61df044..5f77d42 100644 --- a/gtfold-mfe/Makefile.in +++ b/gtfold-mfe/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -39,7 +39,7 @@ subdir = . DIST_COMMON = README $(am__configure_deps) $(include_HEADERS) \ $(srcdir)/Makefile.am $(srcdir)/Makefile.in \ $(srcdir)/gtfold_config.h.in $(top_srcdir)/configure AUTHORS \ - COPYING ChangeLog INSTALL NEWS TODO config.guess config.sub \ + COPYING ChangeLog INSTALL config.guess config.sub \ depcomp install-sh missing ACLOCAL_M4 = $(top_srcdir)/aclocal.m4 am__aclocal_m4_deps = $(top_srcdir)/configure.in @@ -167,7 +167,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -320,7 +319,7 @@ uninstall-includeHEADERS: # (which will cause the Makefiles to be regenerated when you run `make'); # (2) otherwise, pass the desired values on the `make' command line. $(RECURSIVE_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -345,7 +344,7 @@ $(RECURSIVE_TARGETS): fi; test -z "$$fail" $(RECURSIVE_CLEAN_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -509,8 +508,7 @@ distdir: $(DISTFILES) fi; \ done -test -n "$(am__skip_mode_fix)" \ - || find "$(distdir)" -type d ! -perm -755 \ - -exec chmod u+rwx,go+rx {} \; -o \ + || find "$(distdir)" -type d ! -perm -777 -exec chmod a+rwx {} \; -o \ ! -type d ! -perm -444 -links 1 -exec chmod a+r {} \; -o \ ! -type d ! -perm -400 -exec chmod a+r {} \; -o \ ! -type d ! -perm -444 -exec $(install_sh) -c -m a+r {} {} \; \ @@ -554,17 +552,17 @@ dist dist-all: distdir distcheck: dist case '$(DIST_ARCHIVES)' in \ *.tar.gz*) \ - GZIP=$(GZIP_ENV) gzip -dc $(distdir).tar.gz | $(am__untar) ;;\ + GZIP=$(GZIP_ENV) gunzip -c $(distdir).tar.gz | $(am__untar) ;;\ *.tar.bz2*) \ - bzip2 -dc $(distdir).tar.bz2 | $(am__untar) ;;\ + bunzip2 -c $(distdir).tar.bz2 | $(am__untar) ;;\ *.tar.lzma*) \ - lzma -dc $(distdir).tar.lzma | $(am__untar) ;;\ + unlzma -c $(distdir).tar.lzma | $(am__untar) ;;\ *.tar.xz*) \ xz -dc $(distdir).tar.xz | $(am__untar) ;;\ *.tar.Z*) \ uncompress -c $(distdir).tar.Z | $(am__untar) ;;\ *.shar.gz*) \ - GZIP=$(GZIP_ENV) gzip -dc $(distdir).shar.gz | unshar ;;\ + GZIP=$(GZIP_ENV) gunzip -c $(distdir).shar.gz | unshar ;;\ *.zip*) \ unzip $(distdir).zip ;;\ esac diff --git a/gtfold-mfe/README b/gtfold-mfe/README index 34a28f1..0034999 100644 --- a/gtfold-mfe/README +++ b/gtfold-mfe/README @@ -1,14 +1,23 @@ GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction -(C) 2007-2010, David A. Bader - Amrita Mathuriya +(C) 2007-2011, David A. Bader College of Computing, Georgia Institute of Technology Christine E. Heitsch School of Mathematics, Georgia Institute of Technology Stephen C. Harvey School of Biology, Georgia Institute of Technology - Sainath Mallidi - College of Computing, Georgia Institute of Technology + And various contributing authors + +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program. If not, see . The prediction of the correct secondary structures of large RNAs is one of the unsolved challenges of computational molecular biology. @@ -28,8 +37,11 @@ DBI-04-20513. Additionally, the research of Christine E. Heitsch, Ph.D., is supported in part by a Career Award at the Scientific Interface (CASI) from the Burroughs Wellcome Fund (BWF). -Additional contributors to GTfold's implementation include Georgia -Tech visiting students Gregory Nou, Sonny Hernandez, and Manoj Soni. +Additional contributors to GTfold's implementation include +Georgia Tech graduate students Sainath Mallidi, Amrita Mathuriya, +and Prashant Gaurav, undergraduates Joshua Anderson and Andrew Ash +and visiting students Gregory Nou, Sonny Hernandez, Manoj Soni, +and Zsuzsanna Sukosd. INSTALLATION - Please execute the following commands @@ -110,4 +122,18 @@ Version History: 1.16 20 May 2010 Fixed another nasty bug with prohibited constraints handling. Earlier not used to update the WM array if a base pair is prohibited which is causing GTfold to trace partial structure. Some documentation added. - +2.0 11 July 2011 + Optimized the code to enable faster multiloop calculations + Added -d, --dangle to allow treatment of dangling end energies based on user input + Added -m --mismatch to enable terminal mismatch calculations + Added -o, --output, , -w --workdir options to allow to write output files/directories with desired name + Added -p --paramdir to allow user to provide custom parameters + Added -t, --threads to limit number of threads used + Added -v, --verbose to print loop-by-loop energy decomposition and confirm that constraints are satisfied + Added --prefilter to prohibit any basepair which does not have appropriate neighboring nucleotides + such that it could be part of a helix of length INT + Added --rnafold to run GTfold in RNAfold default mode (ViennaPackage version 1.8.5) + Added --unafold to run GTfold in UNAfold default mode (version 3.8) + Added --subopt NUM (Beta only) to produce all suboptimal structures whose energies are within NUM of the MFE + Added --bpp (Beta only) which outputs basepair probabilities based on the partition function + Added --useShape (Beta only) which allows the user to incorporate SHAPE-type data diff --git a/gtfold-mfe/TODO b/gtfold-mfe/TODO deleted file mode 100644 index 366385a..0000000 --- a/gtfold-mfe/TODO +++ /dev/null @@ -1,7 +0,0 @@ -Make single-letter options work - -Partition Function -================== - - - fast inner loops optimization - - factor in dangling energies diff --git a/gtfold-mfe/aclocal.m4 b/gtfold-mfe/aclocal.m4 index ee395e9..eba341b 100644 --- a/gtfold-mfe/aclocal.m4 +++ b/gtfold-mfe/aclocal.m4 @@ -13,8 +13,8 @@ m4_ifndef([AC_AUTOCONF_VERSION], [m4_copy([m4_PACKAGE_VERSION], [AC_AUTOCONF_VERSION])])dnl -m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.68],, -[m4_warning([this file was generated for autoconf 2.68. +m4_if(m4_defn([AC_AUTOCONF_VERSION]), [2.67],, +[m4_warning([this file was generated for autoconf 2.67. You have another version of autoconf. It may work, but is not guaranteed to. If you have problems, you may need to regenerate the build system entirely. To do so, use the procedure documented by the package, typically `autoreconf'.])]) @@ -406,18 +406,6 @@ AC_DEFUN([AM_OUTPUT_DEPENDENCY_COMMANDS], [AMDEP_TRUE="$AMDEP_TRUE" ac_aux_dir="$ac_aux_dir"]) ]) -# Copyright (C) 1996, 1997, 2000, 2001, 2003, 2005 -# Free Software Foundation, Inc. -# -# This file is free software; the Free Software Foundation -# gives unlimited permission to copy and/or distribute it, -# with or without modifications, as long as this notice is preserved. - -# serial 8 - -# AM_CONFIG_HEADER is obsolete. It has been replaced by AC_CONFIG_HEADERS. -AU_DEFUN([AM_CONFIG_HEADER], [AC_CONFIG_HEADERS($@)]) - # Do all the work for Automake. -*- Autoconf -*- # Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, diff --git a/gtfold-mfe/config.guess b/gtfold-mfe/config.guess old mode 100644 new mode 100755 index ca2a03c..c2246a4 --- a/gtfold-mfe/config.guess +++ b/gtfold-mfe/config.guess @@ -1,10 +1,10 @@ #! /bin/sh # Attempt to guess a canonical system name. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 # Free Software Foundation, Inc. -timestamp='2008-01-08' +timestamp='2009-12-30' # This file is free software; you can redistribute it and/or modify it # under the terms of the GNU General Public License as published by @@ -27,16 +27,16 @@ timestamp='2008-01-08' # the same distribution terms that you use for the rest of that program. -# Originally written by Per Bothner . -# Please send patches to . Submit a context -# diff and a properly formatted ChangeLog entry. +# Originally written by Per Bothner. Please send patches (context +# diff format) to and include a ChangeLog +# entry. # # This script attempts to guess a canonical system name similar to # config.sub. If it succeeds, it prints the system name on stdout, and # exits with 0. Otherwise, it exits with 1. # -# The plan is that this can be called by configure scripts if you -# don't specify an explicit build system type. +# You can get the latest version of this script from: +# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD me=`echo "$0" | sed -e 's,.*/,,'` @@ -56,8 +56,9 @@ version="\ GNU config.guess ($timestamp) Originally written by Per Bothner. -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, -2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, +2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free +Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." @@ -170,7 +171,7 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in arm*|i386|m68k|ns32k|sh3*|sparc|vax) eval $set_cc_for_build if echo __ELF__ | $CC_FOR_BUILD -E - 2>/dev/null \ - | grep __ELF__ >/dev/null + | grep -q __ELF__ then # Once all utilities can be ECOFF (netbsdecoff) or a.out (netbsdaout). # Return netbsd for either. FIX? @@ -324,14 +325,33 @@ case "${UNAME_MACHINE}:${UNAME_SYSTEM}:${UNAME_RELEASE}:${UNAME_VERSION}" in case `/usr/bin/uname -p` in sparc) echo sparc-icl-nx7; exit ;; esac ;; + s390x:SunOS:*:*) + echo ${UNAME_MACHINE}-ibm-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + exit ;; sun4H:SunOS:5.*:*) echo sparc-hal-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:5.*:* | tadpole*:SunOS:5.*:*) echo sparc-sun-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; + i86pc:AuroraUX:5.*:* | i86xen:AuroraUX:5.*:*) + echo i386-pc-auroraux${UNAME_RELEASE} + exit ;; i86pc:SunOS:5.*:* | i86xen:SunOS:5.*:*) - echo i386-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` + eval $set_cc_for_build + SUN_ARCH="i386" + # If there is a compiler, see if it is configured for 64-bit objects. + # Note that the Sun cc does not turn __LP64__ into 1 like gcc does. + # This test works for both compilers. + if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then + if (echo '#ifdef __amd64'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + SUN_ARCH="x86_64" + fi + fi + echo ${SUN_ARCH}-pc-solaris2`echo ${UNAME_RELEASE}|sed -e 's/[^.]*//'` exit ;; sun4*:SunOS:6*:*) # According to config.sub, this is the proper way to canonicalize @@ -640,7 +660,7 @@ EOF # => hppa64-hp-hpux11.23 if echo __LP64__ | (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | - grep __LP64__ >/dev/null + grep -q __LP64__ then HP_ARCH="hppa2.0w" else @@ -791,12 +811,12 @@ EOF i*:PW*:*) echo ${UNAME_MACHINE}-pc-pw32 exit ;; - *:Interix*:[3456]*) + *:Interix*:*) case ${UNAME_MACHINE} in x86) echo i586-pc-interix${UNAME_RELEASE} exit ;; - EM64T | authenticamd) + authenticamd | genuineintel | EM64T) echo x86_64-unknown-interix${UNAME_RELEASE} exit ;; IA64) @@ -806,6 +826,9 @@ EOF [345]86:Windows_95:* | [345]86:Windows_98:* | [345]86:Windows_NT:*) echo i${UNAME_MACHINE}-pc-mks exit ;; + 8664:Windows_NT:*) + echo x86_64-pc-mks + exit ;; i*:Windows_NT*:* | Pentium*:Windows_NT*:*) # How do we know it's Interix rather than the generic POSIX subsystem? # It also conflicts with pre-2.0 versions of AT&T UWIN. Should we @@ -835,6 +858,20 @@ EOF i*86:Minix:*:*) echo ${UNAME_MACHINE}-pc-minix exit ;; + alpha:Linux:*:*) + case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in + EV5) UNAME_MACHINE=alphaev5 ;; + EV56) UNAME_MACHINE=alphaev56 ;; + PCA56) UNAME_MACHINE=alphapca56 ;; + PCA57) UNAME_MACHINE=alphapca56 ;; + EV6) UNAME_MACHINE=alphaev6 ;; + EV67) UNAME_MACHINE=alphaev67 ;; + EV68*) UNAME_MACHINE=alphaev68 ;; + esac + objdump --private-headers /bin/sh | grep -q ld.so.1 + if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi + echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + exit ;; arm*:Linux:*:*) eval $set_cc_for_build if echo __ARM_EABI__ | $CC_FOR_BUILD -E - 2>/dev/null \ @@ -857,6 +894,17 @@ EOF frv:Linux:*:*) echo frv-unknown-linux-gnu exit ;; + i*86:Linux:*:*) + LIBC=gnu + eval $set_cc_for_build + sed 's/^ //' << EOF >$dummy.c + #ifdef __dietlibc__ + LIBC=dietlibc + #endif +EOF + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^LIBC'` + echo "${UNAME_MACHINE}-pc-linux-${LIBC}" + exit ;; ia64:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; @@ -866,74 +914,33 @@ EOF m68*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; - mips:Linux:*:*) - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c - #undef CPU - #undef mips - #undef mipsel - #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) - CPU=mipsel - #else - #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) - CPU=mips - #else - CPU= - #endif - #endif -EOF - eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' - /^CPU/{ - s: ::g - p - }'`" - test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } - ;; - mips64:Linux:*:*) + mips:Linux:*:* | mips64:Linux:*:*) eval $set_cc_for_build sed 's/^ //' << EOF >$dummy.c #undef CPU - #undef mips64 - #undef mips64el + #undef ${UNAME_MACHINE} + #undef ${UNAME_MACHINE}el #if defined(__MIPSEL__) || defined(__MIPSEL) || defined(_MIPSEL) || defined(MIPSEL) - CPU=mips64el + CPU=${UNAME_MACHINE}el #else #if defined(__MIPSEB__) || defined(__MIPSEB) || defined(_MIPSEB) || defined(MIPSEB) - CPU=mips64 + CPU=${UNAME_MACHINE} #else CPU= #endif #endif EOF - eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' - /^CPU/{ - s: ::g - p - }'`" + eval `$CC_FOR_BUILD -E $dummy.c 2>/dev/null | grep '^CPU'` test x"${CPU}" != x && { echo "${CPU}-unknown-linux-gnu"; exit; } ;; or32:Linux:*:*) echo or32-unknown-linux-gnu exit ;; - ppc:Linux:*:*) - echo powerpc-unknown-linux-gnu - exit ;; - ppc64:Linux:*:*) - echo powerpc64-unknown-linux-gnu + padre:Linux:*:*) + echo sparc-unknown-linux-gnu exit ;; - alpha:Linux:*:*) - case `sed -n '/^cpu model/s/^.*: \(.*\)/\1/p' < /proc/cpuinfo` in - EV5) UNAME_MACHINE=alphaev5 ;; - EV56) UNAME_MACHINE=alphaev56 ;; - PCA56) UNAME_MACHINE=alphapca56 ;; - PCA57) UNAME_MACHINE=alphapca56 ;; - EV6) UNAME_MACHINE=alphaev6 ;; - EV67) UNAME_MACHINE=alphaev67 ;; - EV68*) UNAME_MACHINE=alphaev68 ;; - esac - objdump --private-headers /bin/sh | grep ld.so.1 >/dev/null - if test "$?" = 0 ; then LIBC="libc1" ; else LIBC="" ; fi - echo ${UNAME_MACHINE}-unknown-linux-gnu${LIBC} + parisc64:Linux:*:* | hppa64:Linux:*:*) + echo hppa64-unknown-linux-gnu exit ;; parisc:Linux:*:* | hppa:Linux:*:*) # Look for CPU level @@ -943,8 +950,11 @@ EOF *) echo hppa-unknown-linux-gnu ;; esac exit ;; - parisc64:Linux:*:* | hppa64:Linux:*:*) - echo hppa64-unknown-linux-gnu + ppc64:Linux:*:*) + echo powerpc64-unknown-linux-gnu + exit ;; + ppc:Linux:*:*) + echo powerpc-unknown-linux-gnu exit ;; s390:Linux:*:* | s390x:Linux:*:*) echo ${UNAME_MACHINE}-ibm-linux @@ -967,69 +977,6 @@ EOF xtensa*:Linux:*:*) echo ${UNAME_MACHINE}-unknown-linux-gnu exit ;; - i*86:Linux:*:*) - # The BFD linker knows what the default object file format is, so - # first see if it will tell us. cd to the root directory to prevent - # problems with other programs or directories called `ld' in the path. - # Set LC_ALL=C to ensure ld outputs messages in English. - ld_supported_targets=`cd /; LC_ALL=C ld --help 2>&1 \ - | sed -ne '/supported targets:/!d - s/[ ][ ]*/ /g - s/.*supported targets: *// - s/ .*// - p'` - case "$ld_supported_targets" in - elf32-i386) - TENTATIVE="${UNAME_MACHINE}-pc-linux-gnu" - ;; - a.out-i386-linux) - echo "${UNAME_MACHINE}-pc-linux-gnuaout" - exit ;; - coff-i386) - echo "${UNAME_MACHINE}-pc-linux-gnucoff" - exit ;; - "") - # Either a pre-BFD a.out linker (linux-gnuoldld) or - # one that does not give us useful --help. - echo "${UNAME_MACHINE}-pc-linux-gnuoldld" - exit ;; - esac - # Determine whether the default compiler is a.out or elf - eval $set_cc_for_build - sed 's/^ //' << EOF >$dummy.c - #include - #ifdef __ELF__ - # ifdef __GLIBC__ - # if __GLIBC__ >= 2 - LIBC=gnu - # else - LIBC=gnulibc1 - # endif - # else - LIBC=gnulibc1 - # endif - #else - #if defined(__INTEL_COMPILER) || defined(__PGI) || defined(__SUNPRO_C) || defined(__SUNPRO_CC) - LIBC=gnu - #else - LIBC=gnuaout - #endif - #endif - #ifdef __dietlibc__ - LIBC=dietlibc - #endif -EOF - eval "`$CC_FOR_BUILD -E $dummy.c 2>/dev/null | sed -n ' - /^LIBC/{ - s: ::g - p - }'`" - test x"${LIBC}" != x && { - echo "${UNAME_MACHINE}-pc-linux-${LIBC}" - exit - } - test x"${TENTATIVE}" != x && { echo "${TENTATIVE}"; exit; } - ;; i*86:DYNIX/ptx:4*:*) # ptx 4.0 does uname -s correctly, with DYNIX/ptx in there. # earlier versions are messed up and put the nodename in both @@ -1058,7 +1005,7 @@ EOF i*86:syllable:*:*) echo ${UNAME_MACHINE}-pc-syllable exit ;; - i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.0*:*) + i*86:LynxOS:2.*:* | i*86:LynxOS:3.[01]*:* | i*86:LynxOS:4.[02]*:*) echo i386-unknown-lynxos${UNAME_RELEASE} exit ;; i*86:*DOS:*:*) @@ -1102,8 +1049,11 @@ EOF pc:*:*:*) # Left here for compatibility: # uname -m prints for DJGPP always 'pc', but it prints nothing about - # the processor, so we play safe by assuming i386. - echo i386-pc-msdosdjgpp + # the processor, so we play safe by assuming i586. + # Note: whatever this is, it MUST be the same as what config.sub + # prints for the "djgpp" host, or else GDB configury will decide that + # this is a cross-build. + echo i586-pc-msdosdjgpp exit ;; Intel:Mach:3*:*) echo i386-pc-mach3 @@ -1141,6 +1091,16 @@ EOF 3[34]??:*:4.0:* | 3[34]??,*:*:4.0:*) /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ && { echo i486-ncr-sysv4; exit; } ;; + NCR*:*:4.2:* | MPRAS*:*:4.2:*) + OS_REL='.3' + test -r /etc/.relid \ + && OS_REL=.`sed -n 's/[^ ]* [^ ]* \([0-9][0-9]\).*/\1/p' < /etc/.relid` + /bin/uname -p 2>/dev/null | grep 86 >/dev/null \ + && { echo i486-ncr-sysv4.3${OS_REL}; exit; } + /bin/uname -p 2>/dev/null | /bin/grep entium >/dev/null \ + && { echo i586-ncr-sysv4.3${OS_REL}; exit; } + /bin/uname -p 2>/dev/null | /bin/grep pteron >/dev/null \ + && { echo i586-ncr-sysv4.3${OS_REL}; exit; } ;; m68*:LynxOS:2.*:* | m68*:LynxOS:3.0*:*) echo m68k-unknown-lynxos${UNAME_RELEASE} exit ;; @@ -1153,7 +1113,7 @@ EOF rs6000:LynxOS:2.*:*) echo rs6000-unknown-lynxos${UNAME_RELEASE} exit ;; - PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.0*:*) + PowerPC:LynxOS:2.*:* | PowerPC:LynxOS:3.[01]*:* | PowerPC:LynxOS:4.[02]*:*) echo powerpc-unknown-lynxos${UNAME_RELEASE} exit ;; SM[BE]S:UNIX_SV:*:*) @@ -1216,6 +1176,9 @@ EOF BePC:BeOS:*:*) # BeOS running on Intel PC compatible. echo i586-pc-beos exit ;; + BePC:Haiku:*:*) # Haiku running on Intel PC compatible. + echo i586-pc-haiku + exit ;; SX-4:SUPER-UX:*:*) echo sx4-nec-superux${UNAME_RELEASE} exit ;; @@ -1243,6 +1206,16 @@ EOF *:Darwin:*:*) UNAME_PROCESSOR=`uname -p` || UNAME_PROCESSOR=unknown case $UNAME_PROCESSOR in + i386) + eval $set_cc_for_build + if [ "$CC_FOR_BUILD" != 'no_compiler_found' ]; then + if (echo '#ifdef __LP64__'; echo IS_64BIT_ARCH; echo '#endif') | \ + (CCOPTS= $CC_FOR_BUILD -E - 2>/dev/null) | \ + grep IS_64BIT_ARCH >/dev/null + then + UNAME_PROCESSOR="x86_64" + fi + fi ;; unknown) UNAME_PROCESSOR=powerpc ;; esac echo ${UNAME_PROCESSOR}-apple-darwin${UNAME_RELEASE} @@ -1324,6 +1297,9 @@ EOF i*86:rdos:*:*) echo ${UNAME_MACHINE}-pc-rdos exit ;; + i*86:AROS:*:*) + echo ${UNAME_MACHINE}-pc-aros + exit ;; esac #echo '(No uname command or uname output not recognized.)' 1>&2 @@ -1484,9 +1460,9 @@ This script, last modified $timestamp, has failed to recognize the operating system you are using. It is advised that you download the most up to date version of the config scripts from - http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess + http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD and - http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub + http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD If the version you run ($0) is already up to date, please send the following data and any information you think might be diff --git a/gtfold-mfe/config.sub b/gtfold-mfe/config.sub old mode 100644 new mode 100755 index 6759825..c2d1257 --- a/gtfold-mfe/config.sub +++ b/gtfold-mfe/config.sub @@ -1,10 +1,10 @@ #! /bin/sh # Configuration validation subroutine script. # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, -# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008 +# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 # Free Software Foundation, Inc. -timestamp='2008-01-16' +timestamp='2010-01-22' # This file is (in principle) common to ALL GNU software. # The presence of a machine in this file suggests that SOME GNU software @@ -32,13 +32,16 @@ timestamp='2008-01-16' # Please send patches to . Submit a context -# diff and a properly formatted ChangeLog entry. +# diff and a properly formatted GNU ChangeLog entry. # # Configuration subroutine to validate and canonicalize a configuration type. # Supply the specified configuration type as an argument. # If it is invalid, we print an error message on stderr and exit with code 1. # Otherwise, we print the canonical config type on stdout and succeed. +# You can get the latest version of this script from: +# http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD + # This file is supposed to be the same for all GNU packages # and recognize all the CPU types, system types and aliases # that are meaningful with *any* GNU software. @@ -72,8 +75,9 @@ Report bugs and patches to ." version="\ GNU config.sub ($timestamp) -Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, -2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. +Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, +2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free +Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE." @@ -122,6 +126,7 @@ maybe_os=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\2/'` case $maybe_os in nto-qnx* | linux-gnu* | linux-dietlibc | linux-newlib* | linux-uclibc* | \ uclinux-uclibc* | uclinux-gnu* | kfreebsd*-gnu* | knetbsd*-gnu* | netbsd*-gnu* | \ + kopensolaris*-gnu* | \ storm-chaos* | os2-emx* | rtmk-nova*) os=-$maybe_os basic_machine=`echo $1 | sed 's/^\(.*\)-\([^-]*-[^-]*\)$/\1/'` @@ -148,10 +153,13 @@ case $os in -convergent* | -ncr* | -news | -32* | -3600* | -3100* | -hitachi* |\ -c[123]* | -convex* | -sun | -crds | -omron* | -dg | -ultra | -tti* | \ -harris | -dolphin | -highlevel | -gould | -cbm | -ns | -masscomp | \ - -apple | -axis | -knuth | -cray) + -apple | -axis | -knuth | -cray | -microblaze) os= basic_machine=$1 ;; + -bluegene*) + os=-cnk + ;; -sim | -cisco | -oki | -wec | -winbond) os= basic_machine=$1 @@ -249,13 +257,16 @@ case $basic_machine in | h8300 | h8500 | hppa | hppa1.[01] | hppa2.0 | hppa2.0[nw] | hppa64 \ | i370 | i860 | i960 | ia64 \ | ip2k | iq2000 \ + | lm32 \ | m32c | m32r | m32rle | m68000 | m68k | m88k \ - | maxq | mb | microblaze | mcore | mep \ + | maxq | mb | microblaze | mcore | mep | metag \ | mips | mipsbe | mipseb | mipsel | mipsle \ | mips16 \ | mips64 | mips64el \ - | mips64vr | mips64vrel \ + | mips64octeon | mips64octeonel \ | mips64orion | mips64orionel \ + | mips64r5900 | mips64r5900el \ + | mips64vr | mips64vrel \ | mips64vr4100 | mips64vr4100el \ | mips64vr4300 | mips64vr4300el \ | mips64vr5000 | mips64vr5000el \ @@ -268,6 +279,7 @@ case $basic_machine in | mipsisa64sr71k | mipsisa64sr71kel \ | mipstx39 | mipstx39el \ | mn10200 | mn10300 \ + | moxie \ | mt \ | msp430 \ | nios | nios2 \ @@ -276,20 +288,22 @@ case $basic_machine in | pdp10 | pdp11 | pj | pjl \ | powerpc | powerpc64 | powerpc64le | powerpcle | ppcbe \ | pyramid \ + | rx \ | score \ - | sh | sh[1234] | sh[24]a | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ + | sh | sh[1234] | sh[24]a | sh[24]aeb | sh[23]e | sh[34]eb | sheb | shbe | shle | sh[1234]le | sh3ele \ | sh64 | sh64le \ | sparc | sparc64 | sparc64b | sparc64v | sparc86x | sparclet | sparclite \ | sparcv8 | sparcv9 | sparcv9b | sparcv9v \ | spu | strongarm \ | tahoe | thumb | tic4x | tic80 | tron \ + | ubicom32 \ | v850 | v850e \ | we32k \ | x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \ - | z8k) + | z8k | z80) basic_machine=$basic_machine-unknown ;; - m6811 | m68hc11 | m6812 | m68hc12) + m6811 | m68hc11 | m6812 | m68hc12 | picochip) # Motorola 68HC11/12. basic_machine=$basic_machine-unknown os=-none @@ -329,14 +343,17 @@ case $basic_machine in | hppa-* | hppa1.[01]-* | hppa2.0-* | hppa2.0[nw]-* | hppa64-* \ | i*86-* | i860-* | i960-* | ia64-* \ | ip2k-* | iq2000-* \ + | lm32-* \ | m32c-* | m32r-* | m32rle-* \ | m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \ - | m88110-* | m88k-* | maxq-* | mcore-* \ + | m88110-* | m88k-* | maxq-* | mcore-* | metag-* | microblaze-* \ | mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \ | mips16-* \ | mips64-* | mips64el-* \ - | mips64vr-* | mips64vrel-* \ + | mips64octeon-* | mips64octeonel-* \ | mips64orion-* | mips64orionel-* \ + | mips64r5900-* | mips64r5900el-* \ + | mips64vr-* | mips64vrel-* \ | mips64vr4100-* | mips64vr4100el-* \ | mips64vr4300-* | mips64vr4300el-* \ | mips64vr5000-* | mips64vr5000el-* \ @@ -357,21 +374,23 @@ case $basic_machine in | pdp10-* | pdp11-* | pj-* | pjl-* | pn-* | power-* \ | powerpc-* | powerpc64-* | powerpc64le-* | powerpcle-* | ppcbe-* \ | pyramid-* \ - | romp-* | rs6000-* \ - | sh-* | sh[1234]-* | sh[24]a-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ + | romp-* | rs6000-* | rx-* \ + | sh-* | sh[1234]-* | sh[24]a-* | sh[24]aeb-* | sh[23]e-* | sh[34]eb-* | sheb-* | shbe-* \ | shle-* | sh[1234]le-* | sh3ele-* | sh64-* | sh64le-* \ | sparc-* | sparc64-* | sparc64b-* | sparc64v-* | sparc86x-* | sparclet-* \ | sparclite-* \ | sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \ | tahoe-* | thumb-* \ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \ + | tile-* | tilegx-* \ | tron-* \ + | ubicom32-* \ | v850-* | v850e-* | vax-* \ | we32k-* \ | x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \ | xstormy16-* | xtensa*-* \ | ymp-* \ - | z8k-*) + | z8k-* | z80-*) ;; # Recognize the basic CPU types without company name, with glob match. xtensa*) @@ -439,6 +458,10 @@ case $basic_machine in basic_machine=m68k-apollo os=-bsd ;; + aros) + basic_machine=i386-pc + os=-aros + ;; aux) basic_machine=m68k-apple os=-aux @@ -455,10 +478,18 @@ case $basic_machine in basic_machine=bfin-`echo $basic_machine | sed 's/^[^-]*-//'` os=-linux ;; + bluegene*) + basic_machine=powerpc-ibm + os=-cnk + ;; c90) basic_machine=c90-cray os=-unicos ;; + cegcc) + basic_machine=arm-unknown + os=-cegcc + ;; convex-c1) basic_machine=c1-convex os=-bsd @@ -526,6 +557,10 @@ case $basic_machine in basic_machine=m88k-motorola os=-sysv3 ;; + dicos) + basic_machine=i686-pc + os=-dicos + ;; djgpp) basic_machine=i586-pc os=-msdosdjgpp @@ -699,6 +734,9 @@ case $basic_machine in basic_machine=ns32k-utek os=-sysv ;; + microblaze) + basic_machine=microblaze-xilinx + ;; mingw32) basic_machine=i386-pc os=-mingw32 @@ -1049,6 +1087,11 @@ case $basic_machine in basic_machine=tic6x-unknown os=-coff ;; + # This must be matched before tile*. + tilegx*) + basic_machine=tilegx-unknown + os=-linux-gnu + ;; tile*) basic_machine=tile-unknown os=-linux-gnu @@ -1128,6 +1171,10 @@ case $basic_machine in basic_machine=z8k-unknown os=-sim ;; + z80-*-coff) + basic_machine=z80-unknown + os=-sim + ;; none) basic_machine=none-none os=-none @@ -1166,7 +1213,7 @@ case $basic_machine in we32k) basic_machine=we32k-att ;; - sh[1234] | sh[24]a | sh[34]eb | sh[1234]le | sh[23]ele) + sh[1234] | sh[24]a | sh[24]aeb | sh[34]eb | sh[1234]le | sh[23]ele) basic_machine=sh-unknown ;; sparc | sparcv8 | sparcv9 | sparcv9b | sparcv9v) @@ -1216,6 +1263,9 @@ case $os in # First match some system type aliases # that might get confused with valid system types. # -solaris* is a basic system type, with this one exception. + -auroraux) + os=-auroraux + ;; -solaris1 | -solaris1.*) os=`echo $os | sed -e 's|solaris1|sunos4|'` ;; @@ -1236,10 +1286,11 @@ case $os in # Each alternative MUST END IN A *, to match a version number. # -sysv* is not here because it comes later, after sysvr4. -gnu* | -bsd* | -mach* | -minix* | -genix* | -ultrix* | -irix* \ - | -*vms* | -sco* | -esix* | -isc* | -aix* | -sunos | -sunos[34]*\ - | -hpux* | -unos* | -osf* | -luna* | -dgux* | -solaris* | -sym* \ + | -*vms* | -sco* | -esix* | -isc* | -aix* | -cnk* | -sunos | -sunos[34]*\ + | -hpux* | -unos* | -osf* | -luna* | -dgux* | -auroraux* | -solaris* \ + | -sym* | -kopensolaris* \ | -amigaos* | -amigados* | -msdos* | -newsos* | -unicos* | -aof* \ - | -aos* \ + | -aos* | -aros* \ | -nindy* | -vxsim* | -vxworks* | -ebmon* | -hms* | -mvs* \ | -clix* | -riscos* | -uniplus* | -iris* | -rtu* | -xenix* \ | -hiux* | -386bsd* | -knetbsd* | -mirbsd* | -netbsd* \ @@ -1248,7 +1299,7 @@ case $os in | -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \ | -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \ | -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \ - | -chorusos* | -chorusrdb* \ + | -chorusos* | -chorusrdb* | -cegcc* \ | -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \ | -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \ | -uxpv* | -beos* | -mpeix* | -udk* \ @@ -1258,7 +1309,7 @@ case $os in | -os2* | -vos* | -palmos* | -uclinux* | -nucleus* \ | -morphos* | -superux* | -rtmk* | -rtmk-nova* | -windiss* \ | -powermax* | -dnix* | -nx6 | -nx7 | -sei* | -dragonfly* \ - | -skyos* | -haiku* | -rdos* | -toppers* | -drops*) + | -skyos* | -haiku* | -rdos* | -toppers* | -drops* | -es*) # Remember, each alternative MUST END IN *, to match a version number. ;; -qnx*) @@ -1388,6 +1439,11 @@ case $os in -zvmoe) os=-zvmoe ;; + -dicos*) + os=-dicos + ;; + -nacl*) + ;; -none) ;; *) @@ -1585,7 +1641,7 @@ case $basic_machine in -sunos*) vendor=sun ;; - -aix*) + -cnk*|-aix*) vendor=ibm ;; -beos*) diff --git a/gtfold-mfe/configure b/gtfold-mfe/configure index c5acafe..e4e3fd1 100755 --- a/gtfold-mfe/configure +++ b/gtfold-mfe/configure @@ -1,22 +1,18 @@ #! /bin/sh # Guess values for system-dependent variables and create Makefiles. -# Generated by GNU Autoconf 2.67 for gtfold 1.18. -# +# Generated by GNU Autoconf 2.63 for gtfold 2.0. # # Copyright (C) 1992, 1993, 1994, 1995, 1996, 1998, 1999, 2000, 2001, -# 2002, 2003, 2004, 2005, 2006, 2007, 2008, 2009, 2010 Free Software -# Foundation, Inc. -# -# +# 2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc. # This configure script is free software; the Free Software Foundation # gives unlimited permission to copy, distribute and modify it. -## -------------------- ## -## M4sh Initialization. ## -## -------------------- ## +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which @@ -24,15 +20,23 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else - case `(set -o) 2>/dev/null` in #( - *posix*) : - set -o posix ;; #( - *) : - ;; + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; esac + fi + + +# PATH needs CR +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + as_nl=' ' export as_nl @@ -40,13 +44,7 @@ export as_nl as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo -# Prefer a ksh shell builtin over an external printf program on Solaris, -# but without wasting forks for bash or zsh. -if test -z "$BASH_VERSION$ZSH_VERSION" \ - && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then - as_echo='print -r --' - as_echo_n='print -rn --' -elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then +if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else @@ -57,7 +55,7 @@ else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; - case $arg in #( + case $arg in *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; @@ -80,6 +78,13 @@ if test "${PATH_SEPARATOR+set}" != set; then } fi +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + # IFS # We need space, tab and new line, in precisely that order. Quoting is @@ -89,15 +94,15 @@ fi IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -case $0 in #(( +case $0 in *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break - done + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done IFS=$as_save_IFS ;; @@ -109,16 +114,12 @@ if test "x$as_myself" = x; then fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 - exit 1 + { (exit 1); exit 1; } fi -# Unset variables that we do not need and which cause bugs (e.g. in -# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" -# suppresses any "Segmentation fault" message there. '((' could -# trigger a bug in pdksh 5.2.14. -for as_var in BASH_ENV ENV MAIL MAILPATH -do eval test x\${$as_var+set} = xset \ - && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +# Work around bugs in pre-3.0 UWIN ksh. +for as_var in ENV MAIL MAILPATH +do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var done PS1='$ ' PS2='> ' @@ -130,299 +131,330 @@ export LC_ALL LANGUAGE=C export LANGUAGE +# Required to use basename. +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi + +if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then + as_basename=basename +else + as_basename=false +fi + + +# Name of the executable. +as_me=`$as_basename -- "$0" || +$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ + X"$0" : 'X\(//\)$' \| \ + X"$0" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X/"$0" | + sed '/^.*\/\([^/][^/]*\)\/*$/{ + s//\1/ + q + } + /^X\/\(\/\/\)$/{ + s//\1/ + q + } + /^X\/\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + # CDPATH. -(unset CDPATH) >/dev/null 2>&1 && unset CDPATH +$as_unset CDPATH + if test "x$CONFIG_SHELL" = x; then - as_bourne_compatible="if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then : - emulate sh - NULLCMD=: - # Pre-4.2 versions of Zsh do word splitting on \${1+\"\$@\"}, which - # is contrary to our usage. Disable this feature. - alias -g '\${1+\"\$@\"}'='\"\$@\"' - setopt NO_GLOB_SUBST + if (eval ":") 2>/dev/null; then + as_have_required=yes else - case \`(set -o) 2>/dev/null\` in #( - *posix*) : - set -o posix ;; #( - *) : - ;; -esac + as_have_required=no fi -" - as_required="as_fn_return () { (exit \$1); } -as_fn_success () { as_fn_return 0; } -as_fn_failure () { as_fn_return 1; } -as_fn_ret_success () { return 0; } -as_fn_ret_failure () { return 1; } + + if test $as_have_required = yes && (eval ": +(as_func_return () { + (exit \$1) +} +as_func_success () { + as_func_return 0 +} +as_func_failure () { + as_func_return 1 +} +as_func_ret_success () { + return 0 +} +as_func_ret_failure () { + return 1 +} exitcode=0 -as_fn_success || { exitcode=1; echo as_fn_success failed.; } -as_fn_failure && { exitcode=1; echo as_fn_failure succeeded.; } -as_fn_ret_success || { exitcode=1; echo as_fn_ret_success failed.; } -as_fn_ret_failure && { exitcode=1; echo as_fn_ret_failure succeeded.; } -if ( set x; as_fn_ret_success y && test x = \"\$1\" ); then : - -else - exitcode=1; echo positional parameters were not saved. -fi -test x\$exitcode = x0 || exit 1" - as_suggested=" as_lineno_1=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_1a=\$LINENO - as_lineno_2=";as_suggested=$as_suggested$LINENO;as_suggested=$as_suggested" as_lineno_2a=\$LINENO - eval 'test \"x\$as_lineno_1'\$as_run'\" != \"x\$as_lineno_2'\$as_run'\" && - test \"x\`expr \$as_lineno_1'\$as_run' + 1\`\" = \"x\$as_lineno_2'\$as_run'\"' || exit 1 -test \$(( 1 + 1 )) = 2 || exit 1" - if (eval "$as_required") 2>/dev/null; then : - as_have_required=yes +if as_func_success; then + : else - as_have_required=no + exitcode=1 + echo as_func_success failed. fi - if test x$as_have_required = xyes && (eval "$as_suggested") 2>/dev/null; then : +if as_func_failure; then + exitcode=1 + echo as_func_failure succeeded. +fi + +if as_func_ret_success; then + : else - as_save_IFS=$IFS; IFS=$PATH_SEPARATOR -as_found=false + exitcode=1 + echo as_func_ret_success failed. +fi + +if as_func_ret_failure; then + exitcode=1 + echo as_func_ret_failure succeeded. +fi + +if ( set x; as_func_ret_success y && test x = \"\$1\" ); then + : +else + exitcode=1 + echo positional parameters were not saved. +fi + +test \$exitcode = 0) || { (exit 1); exit 1; } + +( + as_lineno_1=\$LINENO + as_lineno_2=\$LINENO + test \"x\$as_lineno_1\" != \"x\$as_lineno_2\" && + test \"x\`expr \$as_lineno_1 + 1\`\" = \"x\$as_lineno_2\") || { (exit 1); exit 1; } +") 2> /dev/null; then + : +else + as_candidate_shells= + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in /bin$PATH_SEPARATOR/usr/bin$PATH_SEPARATOR$PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - as_found=: - case $as_dir in #( + case $as_dir in /*) for as_base in sh bash ksh sh5; do - # Try only shells that exist, to save several forks. - as_shell=$as_dir/$as_base - if { test -f "$as_shell" || test -f "$as_shell.exe"; } && - { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$as_shell"; } 2>/dev/null; then : - CONFIG_SHELL=$as_shell as_have_required=yes - if { $as_echo "$as_bourne_compatible""$as_suggested" | as_run=a "$as_shell"; } 2>/dev/null; then : - break 2 -fi -fi + as_candidate_shells="$as_candidate_shells $as_dir/$as_base" done;; esac - as_found=false done -$as_found || { if { test -f "$SHELL" || test -f "$SHELL.exe"; } && - { $as_echo "$as_bourne_compatible""$as_required" | as_run=a "$SHELL"; } 2>/dev/null; then : - CONFIG_SHELL=$SHELL as_have_required=yes -fi; } IFS=$as_save_IFS - if test "x$CONFIG_SHELL" != x; then : - # We cannot yet assume a decent shell, so we have to provide a - # neutralization value for shells without unset; and this also - # works around shells that cannot unset nonexistent variables. - BASH_ENV=/dev/null - ENV=/dev/null - (unset BASH_ENV) >/dev/null 2>&1 && unset BASH_ENV ENV - export CONFIG_SHELL - exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"} -fi + for as_shell in $as_candidate_shells $SHELL; do + # Try only shells that exist, to save several forks. + if { test -f "$as_shell" || test -f "$as_shell.exe"; } && + { ("$as_shell") 2> /dev/null <<\_ASEOF +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; +esac - if test x$as_have_required = xno; then : - $as_echo "$0: This script requires a shell more modern than all" - $as_echo "$0: the shells that I found on your system." - if test x${ZSH_VERSION+set} = xset ; then - $as_echo "$0: In particular, zsh $ZSH_VERSION has bugs and should" - $as_echo "$0: be upgraded to zsh 4.3.4 or later." - else - $as_echo "$0: Please tell bug-autoconf@gnu.org about your system, -$0: including any error possibly output before this -$0: message. Then install a modern shell, or manually run -$0: the script under such a shell if you do have one." - fi - exit 1 -fi fi + + +: +_ASEOF +}; then + CONFIG_SHELL=$as_shell + as_have_required=yes + if { "$as_shell" 2> /dev/null <<\_ASEOF +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then + emulate sh + NULLCMD=: + # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which + # is contrary to our usage. Disable this feature. + alias -g '${1+"$@"}'='"$@"' + setopt NO_GLOB_SUBST +else + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; +esac + fi -SHELL=${CONFIG_SHELL-/bin/sh} -export SHELL -# Unset more variables known to interfere with behavior of common tools. -CLICOLOR_FORCE= GREP_OPTIONS= -unset CLICOLOR_FORCE GREP_OPTIONS -## --------------------- ## -## M4sh Shell Functions. ## -## --------------------- ## -# as_fn_unset VAR -# --------------- -# Portably unset VAR. -as_fn_unset () -{ - { eval $1=; unset $1;} + +: +(as_func_return () { + (exit $1) +} +as_func_success () { + as_func_return 0 +} +as_func_failure () { + as_func_return 1 +} +as_func_ret_success () { + return 0 +} +as_func_ret_failure () { + return 1 } -as_unset=as_fn_unset -# as_fn_set_status STATUS -# ----------------------- -# Set $? to STATUS, without forking. -as_fn_set_status () -{ - return $1 -} # as_fn_set_status +exitcode=0 +if as_func_success; then + : +else + exitcode=1 + echo as_func_success failed. +fi -# as_fn_exit STATUS -# ----------------- -# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. -as_fn_exit () -{ - set +e - as_fn_set_status $1 - exit $1 -} # as_fn_exit - -# as_fn_mkdir_p -# ------------- -# Create "$as_dir" as a directory, including parents if necessary. -as_fn_mkdir_p () -{ +if as_func_failure; then + exitcode=1 + echo as_func_failure succeeded. +fi - case $as_dir in #( - -*) as_dir=./$as_dir;; - esac - test -d "$as_dir" || eval $as_mkdir_p || { - as_dirs= - while :; do - case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( - *) as_qdir=$as_dir;; - esac - as_dirs="'$as_qdir' $as_dirs" - as_dir=`$as_dirname -- "$as_dir" || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ - s//\1/ - q - } - /^X\(\/\/\)[^/].*/{ - s//\1/ - q - } - /^X\(\/\/\)$/{ - s//\1/ - q - } - /^X\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - test -d "$as_dir" && break - done - test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" - - -} # as_fn_mkdir_p -# as_fn_append VAR VALUE -# ---------------------- -# Append the text in VALUE to the end of the definition contained in VAR. Take -# advantage of any shell optimizations that allow amortized linear growth over -# repeated appends, instead of the typical quadratic growth present in naive -# implementations. -if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : - eval 'as_fn_append () - { - eval $1+=\$2 - }' +if as_func_ret_success; then + : else - as_fn_append () - { - eval $1=\$$1\$2 - } -fi # as_fn_append - -# as_fn_arith ARG... -# ------------------ -# Perform arithmetic evaluation on the ARGs, and store the result in the -# global $as_val. Take advantage of shells that can avoid forks. The arguments -# must be portable across $(()) and expr. -if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : - eval 'as_fn_arith () - { - as_val=$(( $* )) - }' + exitcode=1 + echo as_func_ret_success failed. +fi + +if as_func_ret_failure; then + exitcode=1 + echo as_func_ret_failure succeeded. +fi + +if ( set x; as_func_ret_success y && test x = "$1" ); then + : else - as_fn_arith () - { - as_val=`expr "$@" || test $? -eq 1` - } -fi # as_fn_arith + exitcode=1 + echo positional parameters were not saved. +fi +test $exitcode = 0) || { (exit 1); exit 1; } -# as_fn_error STATUS ERROR [LINENO LOG_FD] -# ---------------------------------------- -# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are -# provided, also output the error to LOG_FD, referencing LINENO. Then exit the -# script with STATUS, using 1 if that was 0. -as_fn_error () -{ - as_status=$1; test $as_status -eq 0 && as_status=1 - if test "$4"; then - as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 - fi - $as_echo "$as_me: error: $2" >&2 - as_fn_exit $as_status -} # as_fn_error +( + as_lineno_1=$LINENO + as_lineno_2=$LINENO + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2") || { (exit 1); exit 1; } -if expr a : '\(a\)' >/dev/null 2>&1 && - test "X`expr 00001 : '.*\(...\)'`" = X001; then - as_expr=expr +_ASEOF +}; then + break +fi + +fi + + done + + if test "x$CONFIG_SHELL" != x; then + for as_var in BASH_ENV ENV + do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var + done + export CONFIG_SHELL + exec "$CONFIG_SHELL" "$as_myself" ${1+"$@"} +fi + + + if test $as_have_required = no; then + echo This script requires a shell more modern than all the + echo shells that I found on your system. Please install a + echo modern shell, or manually run the script under such a + echo shell if you do have one. + { (exit 1); exit 1; } +fi + + +fi + +fi + + + +(eval "as_func_return () { + (exit \$1) +} +as_func_success () { + as_func_return 0 +} +as_func_failure () { + as_func_return 1 +} +as_func_ret_success () { + return 0 +} +as_func_ret_failure () { + return 1 +} + +exitcode=0 +if as_func_success; then + : else - as_expr=false + exitcode=1 + echo as_func_success failed. fi -if (basename -- /) >/dev/null 2>&1 && test "X`basename -- / 2>&1`" = "X/"; then - as_basename=basename +if as_func_failure; then + exitcode=1 + echo as_func_failure succeeded. +fi + +if as_func_ret_success; then + : else - as_basename=false + exitcode=1 + echo as_func_ret_success failed. fi -if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then - as_dirname=dirname +if as_func_ret_failure; then + exitcode=1 + echo as_func_ret_failure succeeded. +fi + +if ( set x; as_func_ret_success y && test x = \"\$1\" ); then + : else - as_dirname=false + exitcode=1 + echo positional parameters were not saved. fi -as_me=`$as_basename -- "$0" || -$as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ - X"$0" : 'X\(//\)$' \| \ - X"$0" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X/"$0" | - sed '/^.*\/\([^/][^/]*\)\/*$/{ - s//\1/ - q - } - /^X\/\(\/\/\)$/{ - s//\1/ - q - } - /^X\/\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` +test \$exitcode = 0") || { + echo No shell found that supports shell functions. + echo Please tell bug-autoconf@gnu.org about your system, + echo including any error possibly output before this message. + echo This can help us improve future autoconf versions. + echo Configuration will now proceed without shell functions. +} + -# Avoid depending upon Character Ranges. -as_cr_letters='abcdefghijklmnopqrstuvwxyz' -as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' -as_cr_Letters=$as_cr_letters$as_cr_LETTERS -as_cr_digits='0123456789' -as_cr_alnum=$as_cr_Letters$as_cr_digits + as_lineno_1=$LINENO + as_lineno_2=$LINENO + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || { - as_lineno_1=$LINENO as_lineno_1a=$LINENO - as_lineno_2=$LINENO as_lineno_2a=$LINENO - eval 'test "x$as_lineno_1'$as_run'" != "x$as_lineno_2'$as_run'" && - test "x`expr $as_lineno_1'$as_run' + 1`" = "x$as_lineno_2'$as_run'"' || { - # Blame Lee E. McMahon (1931-1989) for sed's syntax. :-) + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. The first 'sed' inserts a + # line-number line after each line using $LINENO; the second 'sed' + # does the real work. The second script uses 'N' to pair each + # line-number line with the line containing $LINENO, and appends + # trailing '-' during substitution so that $LINENO is not a special + # case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # scripts with optimization help from Paolo Bonzini. Blame Lee + # E. McMahon (1931-1989) for sed's syntax. :-) sed -n ' p /[$]LINENO/= @@ -439,7 +471,8 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits s/-\n.*// ' >$as_me.lineno && chmod +x "$as_me.lineno" || - { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2; as_fn_exit 1; } + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 + { (exit 1); exit 1; }; } # Don't try to exec as it changes $[0], causing all sort of problems # (the dirname of $[0] is not the place where we might find the @@ -449,18 +482,29 @@ as_cr_alnum=$as_cr_Letters$as_cr_digits exit } + +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi + ECHO_C= ECHO_N= ECHO_T= -case `echo -n x` in #((((( +case `echo -n x` in -n*) - case `echo 'xy\c'` in + case `echo 'x\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. - xy) ECHO_C='\c';; - *) echo `echo ksh88 bug on AIX 6.1` > /dev/null - ECHO_T=' ';; + *) ECHO_C='\c';; esac;; *) ECHO_N='-n';; esac +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then @@ -490,7 +534,7 @@ rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null if mkdir -p . 2>/dev/null; then - as_mkdir_p='mkdir -p "$as_dir"' + as_mkdir_p=: else test -d ./-p && rmdir ./-p as_mkdir_p=false @@ -509,10 +553,10 @@ else if test -d "$1"; then test -d "$1/."; else - case $1 in #( + case $1 in -*)set "./$1";; esac; - case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in ???[sx]*):;;*)false;;esac;fi '\'' sh ' @@ -526,11 +570,11 @@ as_tr_cpp="eval sed 'y%*$as_cr_letters%P$as_cr_LETTERS%;s%[^_$as_cr_alnum]%_%g'" as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" -test -n "$DJDIR" || exec 7<&0 &1 + +exec 7<&0 &1 # Name of the host. -# hostname on some systems (SVR3.2, old GNU/Linux) returns a bogus exit status, +# hostname on some systems (SVR3.2, Linux) returns a bogus exit status, # so uname gets run too. ac_hostname=`(hostname || uname -n) 2>/dev/null | sed 1q` @@ -545,14 +589,14 @@ cross_compiling=no subdirs= MFLAGS= MAKEFLAGS= +SHELL=${CONFIG_SHELL-/bin/sh} # Identity of this package. PACKAGE_NAME='gtfold' PACKAGE_TARNAME='gtfold' -PACKAGE_VERSION='1.18' -PACKAGE_STRING='gtfold 1.18' +PACKAGE_VERSION='2.0' +PACKAGE_STRING='gtfold 2.0' PACKAGE_BUGREPORT='' -PACKAGE_URL='' ac_unique_file="README" # Factoring default headers for most tests. @@ -688,7 +732,6 @@ bindir program_transform_name prefix exec_prefix -PACKAGE_URL PACKAGE_BUGREPORT PACKAGE_STRING PACKAGE_VERSION @@ -778,9 +821,8 @@ do fi case $ac_option in - *=?*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; - *=) ac_optarg= ;; - *) ac_optarg=yes ;; + *=*) ac_optarg=`expr "X$ac_option" : '[^=]*=\(.*\)'` ;; + *) ac_optarg=yes ;; esac # Accept the important Cygnus configure options, so we can diagnose typos. @@ -825,7 +867,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*disable-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid feature name: $ac_useropt" + { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -851,7 +894,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*enable-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid feature name: $ac_useropt" + { $as_echo "$as_me: error: invalid feature name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1055,7 +1099,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*with-\([^=]*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid package name: $ac_useropt" + { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1071,7 +1116,8 @@ do ac_useropt=`expr "x$ac_option" : 'x-*without-\(.*\)'` # Reject names that are not valid shell variable names. expr "x$ac_useropt" : ".*[^-+._$as_cr_alnum]" >/dev/null && - as_fn_error $? "invalid package name: $ac_useropt" + { $as_echo "$as_me: error: invalid package name: $ac_useropt" >&2 + { (exit 1); exit 1; }; } ac_useropt_orig=$ac_useropt ac_useropt=`$as_echo "$ac_useropt" | sed 's/[-+.]/_/g'` case $ac_user_opts in @@ -1101,17 +1147,17 @@ do | --x-librar=* | --x-libra=* | --x-libr=* | --x-lib=* | --x-li=* | --x-l=*) x_libraries=$ac_optarg ;; - -*) as_fn_error $? "unrecognized option: \`$ac_option' -Try \`$0 --help' for more information" + -*) { $as_echo "$as_me: error: unrecognized option: $ac_option +Try \`$0 --help' for more information." >&2 + { (exit 1); exit 1; }; } ;; *=*) ac_envvar=`expr "x$ac_option" : 'x\([^=]*\)='` # Reject names that are not valid shell variable names. - case $ac_envvar in #( - '' | [0-9]* | *[!_$as_cr_alnum]* ) - as_fn_error $? "invalid variable name: \`$ac_envvar'" ;; - esac + expr "x$ac_envvar" : ".*[^_$as_cr_alnum]" >/dev/null && + { $as_echo "$as_me: error: invalid variable name: $ac_envvar" >&2 + { (exit 1); exit 1; }; } eval $ac_envvar=\$ac_optarg export $ac_envvar ;; @@ -1128,13 +1174,15 @@ done if test -n "$ac_prev"; then ac_option=--`echo $ac_prev | sed 's/_/-/g'` - as_fn_error $? "missing argument to $ac_option" + { $as_echo "$as_me: error: missing argument to $ac_option" >&2 + { (exit 1); exit 1; }; } fi if test -n "$ac_unrecognized_opts"; then case $enable_option_checking in no) ;; - fatal) as_fn_error $? "unrecognized options: $ac_unrecognized_opts" ;; + fatal) { $as_echo "$as_me: error: unrecognized options: $ac_unrecognized_opts" >&2 + { (exit 1); exit 1; }; } ;; *) $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2 ;; esac fi @@ -1157,7 +1205,8 @@ do [\\/$]* | ?:[\\/]* ) continue;; NONE | '' ) case $ac_var in *prefix ) continue;; esac;; esac - as_fn_error $? "expected an absolute directory name for --$ac_var: $ac_val" + { $as_echo "$as_me: error: expected an absolute directory name for --$ac_var: $ac_val" >&2 + { (exit 1); exit 1; }; } done # There might be people who depend on the old broken behavior: `$host' @@ -1171,8 +1220,8 @@ target=$target_alias if test "x$host_alias" != x; then if test "x$build_alias" = x; then cross_compiling=maybe - $as_echo "$as_me: WARNING: if you wanted to set the --build type, don't use --host. - If a cross compiler is detected then cross compile mode will be used" >&2 + $as_echo "$as_me: WARNING: If you wanted to set the --build type, don't use --host. + If a cross compiler is detected then cross compile mode will be used." >&2 elif test "x$build_alias" != "x$host_alias"; then cross_compiling=yes fi @@ -1187,9 +1236,11 @@ test "$silent" = yes && exec 6>/dev/null ac_pwd=`pwd` && test -n "$ac_pwd" && ac_ls_di=`ls -di .` && ac_pwd_ls_di=`cd "$ac_pwd" && ls -di .` || - as_fn_error $? "working directory cannot be determined" + { $as_echo "$as_me: error: working directory cannot be determined" >&2 + { (exit 1); exit 1; }; } test "X$ac_ls_di" = "X$ac_pwd_ls_di" || - as_fn_error $? "pwd does not report name of working directory" + { $as_echo "$as_me: error: pwd does not report name of working directory" >&2 + { (exit 1); exit 1; }; } # Find the source files, if location was not specified. @@ -1228,11 +1279,13 @@ else fi if test ! -r "$srcdir/$ac_unique_file"; then test "$ac_srcdir_defaulted" = yes && srcdir="$ac_confdir or .." - as_fn_error $? "cannot find sources ($ac_unique_file) in $srcdir" + { $as_echo "$as_me: error: cannot find sources ($ac_unique_file) in $srcdir" >&2 + { (exit 1); exit 1; }; } fi ac_msg="sources are in $srcdir, but \`cd $srcdir' does not work" ac_abs_confdir=`( - cd "$srcdir" && test -r "./$ac_unique_file" || as_fn_error $? "$ac_msg" + cd "$srcdir" && test -r "./$ac_unique_file" || { $as_echo "$as_me: error: $ac_msg" >&2 + { (exit 1); exit 1; }; } pwd)` # When building in place, set srcdir=. if test "$ac_abs_confdir" = "$ac_pwd"; then @@ -1258,7 +1311,7 @@ if test "$ac_init_help" = "long"; then # Omit some internal or obsolete options to make the list less imposing. # This message is too long to be a string in the A/UX 3.1 sh. cat <<_ACEOF -\`configure' configures gtfold 1.18 to adapt to many kinds of systems. +\`configure' configures gtfold 2.0 to adapt to many kinds of systems. Usage: $0 [OPTION]... [VAR=VALUE]... @@ -1272,7 +1325,7 @@ Configuration: --help=short display options specific to this package --help=recursive display the short help of all the included packages -V, --version display version information and exit - -q, --quiet, --silent do not print \`checking ...' messages + -q, --quiet, --silent do not print \`checking...' messages --cache-file=FILE cache test results in FILE [disabled] -C, --config-cache alias for \`--cache-file=config.cache' -n, --no-create do not create output files @@ -1329,7 +1382,7 @@ fi if test -n "$ac_init_help"; then case $ac_init_help in - short | recursive ) echo "Configuration of gtfold 1.18:";; + short | recursive ) echo "Configuration of gtfold 2.0:";; esac cat <<\_ACEOF @@ -1349,537 +1402,93 @@ Some influential environment variables: LDFLAGS linker flags, e.g. -L if you have libraries in a nonstandard directory LIBS libraries to pass to the linker, e.g. -l - CPPFLAGS (Objective) C/C++ preprocessor flags, e.g. -I if + CPPFLAGS C/C++/Objective C preprocessor flags, e.g. -I if you have headers in a nonstandard directory CXX C++ compiler command - CXXFLAGS C++ compiler flags - CPP C preprocessor - -Use these variables to override the choices made by `configure' or to help -it to find libraries and programs with nonstandard names/locations. - -Report bugs to the package provider. -_ACEOF -ac_status=$? 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Invocation command line was +It was created by gtfold $as_me 2.0, which was +generated by GNU Autoconf 2.63. Invocation command line was $ $0 $@ @@ -1915,8 +1524,8 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - $as_echo "PATH: $as_dir" - done + $as_echo "PATH: $as_dir" +done IFS=$as_save_IFS } >&5 @@ -1953,9 +1562,9 @@ do ac_arg=`$as_echo "$ac_arg" | sed "s/'/'\\\\\\\\''/g"` ;; esac case $ac_pass in - 1) as_fn_append ac_configure_args0 " '$ac_arg'" ;; + 1) ac_configure_args0="$ac_configure_args0 '$ac_arg'" ;; 2) - as_fn_append ac_configure_args1 " '$ac_arg'" + ac_configure_args1="$ac_configure_args1 '$ac_arg'" if test $ac_must_keep_next = true; then ac_must_keep_next=false # Got value, back to normal. else @@ -1971,13 +1580,13 @@ do -* ) ac_must_keep_next=true ;; esac fi - as_fn_append ac_configure_args " '$ac_arg'" + ac_configure_args="$ac_configure_args '$ac_arg'" ;; esac done done -{ ac_configure_args0=; unset ac_configure_args0;} -{ ac_configure_args1=; unset ac_configure_args1;} +$as_unset ac_configure_args0 || test "${ac_configure_args0+set}" != set || { ac_configure_args0=; export ac_configure_args0; } +$as_unset ac_configure_args1 || test "${ac_configure_args1+set}" != set || { ac_configure_args1=; export ac_configure_args1; } # When interrupted or exit'd, cleanup temporary files, and complete # config.log. We remove comments because anyway the quotes in there @@ -1989,9 +1598,11 @@ trap 'exit_status=$? { echo - $as_echo "## ---------------- ## + cat <<\_ASBOX +## ---------------- ## ## Cache variables. ## -## ---------------- ##" +## ---------------- ## +_ASBOX echo # The following way of writing the cache mishandles newlines in values, ( @@ -2000,13 +1611,13 @@ trap 'exit_status=$? case $ac_val in #( *${as_nl}*) case $ac_var in #( - *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 + *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( - *) { eval $ac_var=; unset $ac_var;} ;; + *) $as_unset $ac_var ;; esac ;; esac done @@ -2025,9 +1636,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; ) echo - $as_echo "## ----------------- ## + cat <<\_ASBOX +## ----------------- ## ## Output variables. ## -## ----------------- ##" +## ----------------- ## +_ASBOX echo for ac_var in $ac_subst_vars do @@ -2040,9 +1653,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; echo if test -n "$ac_subst_files"; then - $as_echo "## ------------------- ## + cat <<\_ASBOX +## ------------------- ## ## File substitutions. ## -## ------------------- ##" +## ------------------- ## +_ASBOX echo for ac_var in $ac_subst_files do @@ -2056,9 +1671,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; fi if test -s confdefs.h; then - $as_echo "## ----------- ## + cat <<\_ASBOX +## ----------- ## ## confdefs.h. ## -## ----------- ##" +## ----------- ## +_ASBOX echo cat confdefs.h echo @@ -2072,39 +1689,37 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; exit $exit_status ' 0 for ac_signal in 1 2 13 15; do - trap 'ac_signal='$ac_signal'; as_fn_exit 1' $ac_signal + trap 'ac_signal='$ac_signal'; { (exit 1); exit 1; }' $ac_signal done ac_signal=0 # confdefs.h avoids OS command line length limits that DEFS can exceed. rm -f -r conftest* confdefs.h -$as_echo "/* confdefs.h */" > confdefs.h - # Predefined preprocessor variables. cat >>confdefs.h <<_ACEOF #define PACKAGE_NAME "$PACKAGE_NAME" _ACEOF + cat >>confdefs.h <<_ACEOF #define PACKAGE_TARNAME "$PACKAGE_TARNAME" _ACEOF + cat >>confdefs.h <<_ACEOF #define PACKAGE_VERSION "$PACKAGE_VERSION" _ACEOF + cat >>confdefs.h <<_ACEOF #define PACKAGE_STRING "$PACKAGE_STRING" _ACEOF -cat >>confdefs.h <<_ACEOF -#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" -_ACEOF cat >>confdefs.h <<_ACEOF -#define PACKAGE_URL "$PACKAGE_URL" +#define PACKAGE_BUGREPORT "$PACKAGE_BUGREPORT" _ACEOF @@ -2113,12 +1728,7 @@ _ACEOF ac_site_file1=NONE ac_site_file2=NONE if test -n "$CONFIG_SITE"; then - # We do not want a PATH search for config.site. - case $CONFIG_SITE in #(( - -*) ac_site_file1=./$CONFIG_SITE;; - */*) ac_site_file1=$CONFIG_SITE;; - *) ac_site_file1=./$CONFIG_SITE;; - esac + ac_site_file1=$CONFIG_SITE elif test "x$prefix" != xNONE; then ac_site_file1=$prefix/share/config.site ac_site_file2=$prefix/etc/config.site @@ -2129,23 +1739,19 @@ fi for ac_site_file in "$ac_site_file1" "$ac_site_file2" do test "x$ac_site_file" = xNONE && continue - if test /dev/null != "$ac_site_file" && test -r "$ac_site_file"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: loading site script $ac_site_file" >&5 + if test -r "$ac_site_file"; then + { $as_echo "$as_me:$LINENO: loading site script $ac_site_file" >&5 $as_echo "$as_me: loading site script $ac_site_file" >&6;} sed 's/^/| /' "$ac_site_file" >&5 - . "$ac_site_file" \ - || { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 -$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "failed to load site script $ac_site_file -See \`config.log' for more details" "$LINENO" 5 ; } + . "$ac_site_file" fi done if test -r "$cache_file"; then - # Some versions of bash will fail to source /dev/null (special files - # actually), so we avoid doing that. DJGPP emulates it as a regular file. - if test /dev/null != "$cache_file" && test -f "$cache_file"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: loading cache $cache_file" >&5 + # Some versions of bash will fail to source /dev/null (special + # files actually), so we avoid doing that. + if test -f "$cache_file"; then + { $as_echo "$as_me:$LINENO: loading cache $cache_file" >&5 $as_echo "$as_me: loading cache $cache_file" >&6;} case $cache_file in [\\/]* | ?:[\\/]* ) . "$cache_file";; @@ -2153,7 +1759,7 @@ $as_echo "$as_me: loading cache $cache_file" >&6;} esac fi else - { $as_echo "$as_me:${as_lineno-$LINENO}: creating cache $cache_file" >&5 + { $as_echo "$as_me:$LINENO: creating cache $cache_file" >&5 $as_echo "$as_me: creating cache $cache_file" >&6;} >$cache_file fi @@ -2168,11 +1774,11 @@ for ac_var in $ac_precious_vars; do eval ac_new_val=\$ac_env_${ac_var}_value case $ac_old_set,$ac_new_set in set,) - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 + { $as_echo "$as_me:$LINENO: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&5 $as_echo "$as_me: error: \`$ac_var' was set to \`$ac_old_val' in the previous run" >&2;} ac_cache_corrupted=: ;; ,set) - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' was not set in the previous run" >&5 + { $as_echo "$as_me:$LINENO: error: \`$ac_var' was not set in the previous run" >&5 $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_cache_corrupted=: ;; ,);; @@ -2182,17 +1788,17 @@ $as_echo "$as_me: error: \`$ac_var' was not set in the previous run" >&2;} ac_old_val_w=`echo x $ac_old_val` ac_new_val_w=`echo x $ac_new_val` if test "$ac_old_val_w" != "$ac_new_val_w"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: error: \`$ac_var' has changed since the previous run:" >&5 + { $as_echo "$as_me:$LINENO: error: \`$ac_var' has changed since the previous run:" >&5 $as_echo "$as_me: error: \`$ac_var' has changed since the previous run:" >&2;} ac_cache_corrupted=: else - { $as_echo "$as_me:${as_lineno-$LINENO}: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 + { $as_echo "$as_me:$LINENO: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&5 $as_echo "$as_me: warning: ignoring whitespace changes in \`$ac_var' since the previous run:" >&2;} eval $ac_var=\$ac_old_val fi - { $as_echo "$as_me:${as_lineno-$LINENO}: former value: \`$ac_old_val'" >&5 + { $as_echo "$as_me:$LINENO: former value: \`$ac_old_val'" >&5 $as_echo "$as_me: former value: \`$ac_old_val'" >&2;} - { $as_echo "$as_me:${as_lineno-$LINENO}: current value: \`$ac_new_val'" >&5 + { $as_echo "$as_me:$LINENO: current value: \`$ac_new_val'" >&5 $as_echo "$as_me: current value: \`$ac_new_val'" >&2;} fi;; esac @@ -2204,20 +1810,43 @@ $as_echo "$as_me: current value: \`$ac_new_val'" >&2;} esac case " $ac_configure_args " in *" '$ac_arg' "*) ;; # Avoid dups. Use of quotes ensures accuracy. - *) as_fn_append ac_configure_args " '$ac_arg'" ;; + *) ac_configure_args="$ac_configure_args '$ac_arg'" ;; esac fi done if $ac_cache_corrupted; then - { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 + { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} - { $as_echo "$as_me:${as_lineno-$LINENO}: error: changes in the environment can compromise the build" >&5 + { $as_echo "$as_me:$LINENO: error: changes in the environment can compromise the build" >&5 $as_echo "$as_me: error: changes in the environment can compromise the build" >&2;} - as_fn_error $? "run \`make distclean' and/or \`rm $cache_file' and start over" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&5 +$as_echo "$as_me: error: run \`make distclean' and/or \`rm $cache_file' and start over" >&2;} + { (exit 1); exit 1; }; } fi -## -------------------- ## -## Main body of script. ## -## -------------------- ## + + + + + + + + + + + + + + + + + + + + + + + + ac_ext=c ac_cpp='$CPP $CPPFLAGS' @@ -2249,7 +1878,9 @@ for ac_dir in "$srcdir" "$srcdir/.." "$srcdir/../.."; do fi done if test -z "$ac_aux_dir"; then - as_fn_error $? "cannot find install-sh, install.sh, or shtool in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&5 +$as_echo "$as_me: error: cannot find install-sh or install.sh in \"$srcdir\" \"$srcdir/..\" \"$srcdir/../..\"" >&2;} + { (exit 1); exit 1; }; } fi # These three variables are undocumented and unsupported, @@ -2263,27 +1894,35 @@ ac_configure="$SHELL $ac_aux_dir/configure" # Please don't use this var. # Make sure we can run config.sub. $SHELL "$ac_aux_dir/config.sub" sun4 >/dev/null 2>&1 || - as_fn_error $? "cannot run $SHELL $ac_aux_dir/config.sub" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: cannot run $SHELL $ac_aux_dir/config.sub" >&5 +$as_echo "$as_me: error: cannot run $SHELL $ac_aux_dir/config.sub" >&2;} + { (exit 1); exit 1; }; } -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking build system type" >&5 +{ $as_echo "$as_me:$LINENO: checking build system type" >&5 $as_echo_n "checking build system type... " >&6; } -if test "${ac_cv_build+set}" = set; then : +if test "${ac_cv_build+set}" = set; then $as_echo_n "(cached) " >&6 else ac_build_alias=$build_alias test "x$ac_build_alias" = x && ac_build_alias=`$SHELL "$ac_aux_dir/config.guess"` test "x$ac_build_alias" = x && - as_fn_error $? "cannot guess build type; you must specify one" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: cannot guess build type; you must specify one" >&5 +$as_echo "$as_me: error: cannot guess build type; you must specify one" >&2;} + { (exit 1); exit 1; }; } ac_cv_build=`$SHELL "$ac_aux_dir/config.sub" $ac_build_alias` || - as_fn_error $? "$SHELL $ac_aux_dir/config.sub $ac_build_alias failed" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $ac_build_alias failed" >&2;} + { (exit 1); exit 1; }; } fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_build" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_build" >&5 $as_echo "$ac_cv_build" >&6; } case $ac_cv_build in *-*-*) ;; -*) as_fn_error $? "invalid value of canonical build" "$LINENO" 5 ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical build" >&5 +$as_echo "$as_me: error: invalid value of canonical build" >&2;} + { (exit 1); exit 1; }; };; esac build=$ac_cv_build ac_save_IFS=$IFS; IFS='-' @@ -2299,24 +1938,28 @@ IFS=$ac_save_IFS case $build_os in *\ *) build_os=`echo "$build_os" | sed 's/ /-/g'`;; esac -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking host system type" >&5 +{ $as_echo "$as_me:$LINENO: checking host system type" >&5 $as_echo_n "checking host system type... " >&6; } -if test "${ac_cv_host+set}" = set; then : +if test "${ac_cv_host+set}" = set; then $as_echo_n "(cached) " >&6 else if test "x$host_alias" = x; then ac_cv_host=$ac_cv_build else ac_cv_host=`$SHELL "$ac_aux_dir/config.sub" $host_alias` || - as_fn_error $? "$SHELL $ac_aux_dir/config.sub $host_alias failed" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $host_alias failed" >&2;} + { (exit 1); exit 1; }; } fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_host" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_host" >&5 $as_echo "$ac_cv_host" >&6; } case $ac_cv_host in *-*-*) ;; -*) as_fn_error $? "invalid value of canonical host" "$LINENO" 5 ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical host" >&5 +$as_echo "$as_me: error: invalid value of canonical host" >&2;} + { (exit 1); exit 1; }; };; esac host=$ac_cv_host ac_save_IFS=$IFS; IFS='-' @@ -2332,24 +1975,28 @@ IFS=$ac_save_IFS case $host_os in *\ *) host_os=`echo "$host_os" | sed 's/ /-/g'`;; esac -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking target system type" >&5 +{ $as_echo "$as_me:$LINENO: checking target system type" >&5 $as_echo_n "checking target system type... " >&6; } -if test "${ac_cv_target+set}" = set; then : +if test "${ac_cv_target+set}" = set; then $as_echo_n "(cached) " >&6 else if test "x$target_alias" = x; then ac_cv_target=$ac_cv_host else ac_cv_target=`$SHELL "$ac_aux_dir/config.sub" $target_alias` || - as_fn_error $? "$SHELL $ac_aux_dir/config.sub $target_alias failed" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&5 +$as_echo "$as_me: error: $SHELL $ac_aux_dir/config.sub $target_alias failed" >&2;} + { (exit 1); exit 1; }; } fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_target" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_target" >&5 $as_echo "$ac_cv_target" >&6; } case $ac_cv_target in *-*-*) ;; -*) as_fn_error $? "invalid value of canonical target" "$LINENO" 5 ;; +*) { { $as_echo "$as_me:$LINENO: error: invalid value of canonical target" >&5 +$as_echo "$as_me: error: invalid value of canonical target" >&2;} + { (exit 1); exit 1; }; };; esac target=$ac_cv_target ac_save_IFS=$IFS; IFS='-' @@ -2372,7 +2019,6 @@ test -n "$target_alias" && NONENONEs,x,x, && program_prefix=${target_alias}- - am__api_version='1.11' # Find a good install program. We prefer a C program (faster), @@ -2389,10 +2035,10 @@ am__api_version='1.11' # OS/2's system install, which has a completely different semantic # ./install, which can be erroneously created by make from ./install.sh. # Reject install programs that cannot install multiple files. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a BSD-compatible install" >&5 +{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 $as_echo_n "checking for a BSD-compatible install... " >&6; } if test -z "$INSTALL"; then -if test "${ac_cv_path_install+set}" = set; then : +if test "${ac_cv_path_install+set}" = set; then $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -2400,11 +2046,11 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - # Account for people who put trailing slashes in PATH elements. -case $as_dir/ in #(( - ./ | .// | /[cC]/* | \ + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ - ?:[\\/]os2[\\/]install[\\/]* | ?:[\\/]OS2[\\/]INSTALL[\\/]* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ /usr/ucb/* ) ;; *) # OSF1 and SCO ODT 3.0 have their own names for install. @@ -2441,7 +2087,7 @@ case $as_dir/ in #(( ;; esac - done +done IFS=$as_save_IFS rm -rf conftest.one conftest.two conftest.dir @@ -2457,7 +2103,7 @@ fi INSTALL=$ac_install_sh fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $INSTALL" >&5 +{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5 $as_echo "$INSTALL" >&6; } # Use test -z because SunOS4 sh mishandles braces in ${var-val}. @@ -2468,7 +2114,7 @@ test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether build environment is sane" >&5 +{ $as_echo "$as_me:$LINENO: checking whether build environment is sane" >&5 $as_echo_n "checking whether build environment is sane... " >&6; } # Just in case sleep 1 @@ -2479,11 +2125,15 @@ am_lf=' ' case `pwd` in *[\\\"\#\$\&\'\`$am_lf]*) - as_fn_error $? "unsafe absolute working directory name" "$LINENO" 5 ;; + { { $as_echo "$as_me:$LINENO: error: unsafe absolute working directory name" >&5 +$as_echo "$as_me: error: unsafe absolute working directory name" >&2;} + { (exit 1); exit 1; }; };; esac case $srcdir in *[\\\"\#\$\&\'\`$am_lf\ \ ]*) - as_fn_error $? "unsafe srcdir value: \`$srcdir'" "$LINENO" 5 ;; + { { $as_echo "$as_me:$LINENO: error: unsafe srcdir value: \`$srcdir'" >&5 +$as_echo "$as_me: error: unsafe srcdir value: \`$srcdir'" >&2;} + { (exit 1); exit 1; }; };; esac # Do `set' in a subshell so we don't clobber the current shell's @@ -2505,8 +2155,11 @@ if ( # if, for instance, CONFIG_SHELL is bash and it inherits a # broken ls alias from the environment. This has actually # happened. Such a system could not be considered "sane". - as_fn_error $? "ls -t appears to fail. Make sure there is not a broken -alias in your environment" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: ls -t appears to fail. Make sure there is not a broken +alias in your environment" >&5 +$as_echo "$as_me: error: ls -t appears to fail. Make sure there is not a broken +alias in your environment" >&2;} + { (exit 1); exit 1; }; } fi test "$2" = conftest.file @@ -2515,10 +2168,13 @@ then # Ok. : else - as_fn_error $? "newly created file is older than distributed files! -Check your system clock" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: newly created file is older than distributed files! +Check your system clock" >&5 +$as_echo "$as_me: error: newly created file is older than distributed files! +Check your system clock" >&2;} + { (exit 1); exit 1; }; } fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +{ $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } test "$program_prefix" != NONE && program_transform_name="s&^&$program_prefix&;$program_transform_name" @@ -2546,7 +2202,7 @@ if eval "$MISSING --run true"; then am_missing_run="$MISSING --run " else am_missing_run= - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: \`missing' script is too old or missing" >&5 + { $as_echo "$as_me:$LINENO: WARNING: \`missing' script is too old or missing" >&5 $as_echo "$as_me: WARNING: \`missing' script is too old or missing" >&2;} fi @@ -2567,9 +2223,9 @@ if test "$cross_compiling" != no; then if test -n "$ac_tool_prefix"; then # Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args. set dummy ${ac_tool_prefix}strip; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_STRIP+set}" = set; then : +if test "${ac_cv_prog_STRIP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$STRIP"; then @@ -2580,24 +2236,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_STRIP="${ac_tool_prefix}strip" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi STRIP=$ac_cv_prog_STRIP if test -n "$STRIP"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $STRIP" >&5 + { $as_echo "$as_me:$LINENO: result: $STRIP" >&5 $as_echo "$STRIP" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2607,9 +2263,9 @@ if test -z "$ac_cv_prog_STRIP"; then ac_ct_STRIP=$STRIP # Extract the first word of "strip", so it can be a program name with args. set dummy strip; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then : +if test "${ac_cv_prog_ac_ct_STRIP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_STRIP"; then @@ -2620,24 +2276,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_STRIP="strip" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi ac_ct_STRIP=$ac_cv_prog_ac_ct_STRIP if test -n "$ac_ct_STRIP"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_STRIP" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_ct_STRIP" >&5 $as_echo "$ac_ct_STRIP" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2646,7 +2302,7 @@ fi else case $cross_compiling:$ac_tool_warned in yes:) -{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac @@ -2659,10 +2315,10 @@ fi fi INSTALL_STRIP_PROGRAM="\$(install_sh) -c -s" -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for a thread-safe mkdir -p" >&5 +{ $as_echo "$as_me:$LINENO: checking for a thread-safe mkdir -p" >&5 $as_echo_n "checking for a thread-safe mkdir -p... " >&6; } if test -z "$MKDIR_P"; then - if test "${ac_cv_path_mkdir+set}" = set; then : + if test "${ac_cv_path_mkdir+set}" = set; then $as_echo_n "(cached) " >&6 else as_save_IFS=$IFS; IFS=$PATH_SEPARATOR @@ -2670,7 +2326,7 @@ for as_dir in $PATH$PATH_SEPARATOR/opt/sfw/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_prog in mkdir gmkdir; do + for ac_prog in mkdir gmkdir; do for ac_exec_ext in '' $ac_executable_extensions; do { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; } || continue case `"$as_dir/$ac_prog$ac_exec_ext" --version 2>&1` in #( @@ -2682,12 +2338,11 @@ do esac done done - done +done IFS=$as_save_IFS fi - test -d ./--version && rmdir ./--version if test "${ac_cv_path_mkdir+set}" = set; then MKDIR_P="$ac_cv_path_mkdir -p" else @@ -2695,10 +2350,11 @@ fi # value for MKDIR_P within a source directory, because that will # break other packages using the cache if that directory is # removed, or if the value is a relative name. + test -d ./--version && rmdir ./--version MKDIR_P="$ac_install_sh -d" fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $MKDIR_P" >&5 +{ $as_echo "$as_me:$LINENO: result: $MKDIR_P" >&5 $as_echo "$MKDIR_P" >&6; } mkdir_p="$MKDIR_P" @@ -2711,9 +2367,9 @@ for ac_prog in gawk mawk nawk awk do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_AWK+set}" = set; then : +if test "${ac_cv_prog_AWK+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$AWK"; then @@ -2724,24 +2380,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_AWK="$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi AWK=$ac_cv_prog_AWK if test -n "$AWK"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $AWK" >&5 + { $as_echo "$as_me:$LINENO: result: $AWK" >&5 $as_echo "$AWK" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2749,11 +2405,11 @@ fi test -n "$AWK" && break done -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether ${MAKE-make} sets \$(MAKE)" >&5 +{ $as_echo "$as_me:$LINENO: checking whether ${MAKE-make} sets \$(MAKE)" >&5 $as_echo_n "checking whether ${MAKE-make} sets \$(MAKE)... " >&6; } set x ${MAKE-make} ac_make=`$as_echo "$2" | sed 's/+/p/g; s/[^a-zA-Z0-9_]/_/g'` -if eval "test \"\${ac_cv_prog_make_${ac_make}_set+set}\"" = set; then : +if { as_var=ac_cv_prog_make_${ac_make}_set; eval "test \"\${$as_var+set}\" = set"; }; then $as_echo_n "(cached) " >&6 else cat >conftest.make <<\_ACEOF @@ -2761,7 +2417,7 @@ SHELL = /bin/sh all: @echo '@@@%%%=$(MAKE)=@@@%%%' _ACEOF -# GNU make sometimes prints "make[1]: Entering ...", which would confuse us. +# GNU make sometimes prints "make[1]: Entering...", which would confuse us. case `${MAKE-make} -f conftest.make 2>/dev/null` in *@@@%%%=?*=@@@%%%*) eval ac_cv_prog_make_${ac_make}_set=yes;; @@ -2771,11 +2427,11 @@ esac rm -f conftest.make fi if eval test \$ac_cv_prog_make_${ac_make}_set = yes; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } SET_MAKE= else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } SET_MAKE="MAKE=${MAKE-make}" fi @@ -2795,7 +2451,9 @@ if test "`cd $srcdir && pwd`" != "`pwd`"; then am__isrc=' -I$(srcdir)' # test to see if srcdir already configured if test -f $srcdir/config.status; then - as_fn_error $? "source directory already configured; run \"make distclean\" there first" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: source directory already configured; run \"make distclean\" there first" >&5 +$as_echo "$as_me: error: source directory already configured; run \"make distclean\" there first" >&2;} + { (exit 1); exit 1; }; } fi fi @@ -2811,7 +2469,7 @@ fi # Define the identity of the package. PACKAGE='gtfold' - VERSION='1.18' + VERSION='2.0' cat >>confdefs.h <<_ACEOF @@ -2853,11 +2511,13 @@ am__tar='${AMTAR} chof - "$$tardir"'; am__untar='${AMTAR} xf -' # Check whether --enable-64bit was given. -if test "${enable_64bit+set}" = set; then : +if test "${enable_64bit+set}" = set; then enableval=$enable_64bit; case "${enableval}" in "" | y | ye | yes) gtfold_cv_enable_64bit=yes ;; n | no) gtfold_cv_enable_64bit=no ;; - *) as_fn_error $? "bad value ${enableval} for --enable-64bit" "$LINENO" 5 ;; + *) { { $as_echo "$as_me:$LINENO: error: bad value ${enableval} for --enable-64bit" >&5 +$as_echo "$as_me: error: bad value ${enableval} for --enable-64bit" >&2;} + { (exit 1); exit 1; }; } ;; esac else gtfold_cv_enable_64bit=no @@ -2888,9 +2548,9 @@ if test -n "$ac_tool_prefix"; then do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CC+set}" = set; then : +if test "${ac_cv_prog_CC+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$CC"; then @@ -2901,24 +2561,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CC="$ac_tool_prefix$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi CC=$ac_cv_prog_CC if test -n "$CC"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CC" >&5 + { $as_echo "$as_me:$LINENO: result: $CC" >&5 $as_echo "$CC" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2932,9 +2592,9 @@ if test -z "$CC"; then do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_ac_ct_CC+set}" = set; then : +if test "${ac_cv_prog_ac_ct_CC+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CC"; then @@ -2945,24 +2605,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CC="$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi ac_ct_CC=$ac_cv_prog_ac_ct_CC if test -n "$ac_ct_CC"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CC" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_ct_CC" >&5 $as_echo "$ac_ct_CC" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -2975,7 +2635,7 @@ done else case $cross_compiling:$ac_tool_warned in yes:) -{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac @@ -2984,37 +2644,57 @@ esac fi -test -z "$CC" && { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +test -z "$CC" && { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "no acceptable C compiler found in \$PATH -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: no acceptable C compiler found in \$PATH +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } # Provide some information about the compiler. -$as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler version" >&5 +$as_echo "$as_me:$LINENO: checking for C compiler version" >&5 set X $ac_compile ac_compiler=$2 -for ac_option in --version -v -V -qversion; do - { { ac_try="$ac_compiler $ac_option >&5" +{ (ac_try="$ac_compiler --version >&5" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_compiler $ac_option >&5") 2>conftest.err +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler --version >&5") 2>&5 ac_status=$? - if test -s conftest.err; then - sed '10a\ -... rest of stderr output deleted ... - 10q' conftest.err >conftest.er1 - cat conftest.er1 >&5 - fi - rm -f conftest.er1 conftest.err - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; } -done + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -v >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -v >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -V >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -V >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3030,8 +2710,8 @@ ac_clean_files="$ac_clean_files a.out a.out.dSYM a.exe b.out" # Try to create an executable without -o first, disregard a.out. # It will help us diagnose broken compilers, and finding out an intuition # of exeext. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether the C compiler works" >&5 -$as_echo_n "checking whether the C compiler works... " >&6; } +{ $as_echo "$as_me:$LINENO: checking for C compiler default output file name" >&5 +$as_echo_n "checking for C compiler default output file name... " >&6; } ac_link_default=`$as_echo "$ac_link" | sed 's/ -o *conftest[^ ]*//'` # The possible output files: @@ -3047,17 +2727,17 @@ do done rm -f $ac_rmfiles -if { { ac_try="$ac_link_default" +if { (ac_try="$ac_link_default" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 (eval "$ac_link_default") 2>&5 ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; then : + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then # Autoconf-2.13 could set the ac_cv_exeext variable to `no'. # So ignore a value of `no', otherwise this would lead to `EXEEXT = no' # in a Makefile. We should not override ac_cv_exeext if it was cached, @@ -3074,7 +2754,7 @@ do # certainly right. break;; *.* ) - if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; + if test "${ac_cv_exeext+set}" = set && test "$ac_cv_exeext" != no; then :; else ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` fi @@ -3093,132 +2773,124 @@ test "$ac_cv_exeext" = no && ac_cv_exeext= else ac_file='' fi -if test -z "$ac_file"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 -$as_echo "no" >&6; } -$as_echo "$as_me: failed program was:" >&5 -sed 's/^/| /' conftest.$ac_ext >&5 -{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 -$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error 77 "C compiler cannot create executables -See \`config.log' for more details" "$LINENO" 5 ; } -else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 -$as_echo "yes" >&6; } -fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for C compiler default output file name" >&5 -$as_echo_n "checking for C compiler default output file name... " >&6; } -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_file" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_file" >&5 $as_echo "$ac_file" >&6; } -ac_exeext=$ac_cv_exeext +if test -z "$ac_file"; then + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 -rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out -ac_clean_files=$ac_clean_files_save -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of executables" >&5 -$as_echo_n "checking for suffix of executables... " >&6; } -if { { ac_try="$ac_link" -case "(($ac_try" in - *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; - *) ac_try_echo=$ac_try;; -esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_link") 2>&5 - ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; then : - # If both `conftest.exe' and `conftest' are `present' (well, observable) -# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will -# work properly (i.e., refer to `conftest.exe'), while it won't with -# `rm'. -for ac_file in conftest.exe conftest conftest.*; do - test -f "$ac_file" || continue - case $ac_file in - *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; - *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` - break;; - * ) break;; - esac -done -else - { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "cannot compute suffix of executables: cannot compile and link -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: C compiler cannot create executables +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: C compiler cannot create executables +See \`config.log' for more details." >&2;} + { (exit 77); exit 77; }; }; } fi -rm -f conftest conftest$ac_cv_exeext -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_exeext" >&5 -$as_echo "$ac_cv_exeext" >&6; } -rm -f conftest.$ac_ext -EXEEXT=$ac_cv_exeext -ac_exeext=$EXEEXT -cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ -#include -int -main () -{ -FILE *f = fopen ("conftest.out", "w"); - return ferror (f) || fclose (f) != 0; +ac_exeext=$ac_cv_exeext - ; - return 0; -} -_ACEOF -ac_clean_files="$ac_clean_files conftest.out" # Check that the compiler produces executables we can run. If not, either # the compiler is broken, or we cross compile. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are cross compiling" >&5 -$as_echo_n "checking whether we are cross compiling... " >&6; } +{ $as_echo "$as_me:$LINENO: checking whether the C compiler works" >&5 +$as_echo_n "checking whether the C compiler works... " >&6; } +# FIXME: These cross compiler hacks should be removed for Autoconf 3.0 +# If not cross compiling, check that we can run a simple program. if test "$cross_compiling" != yes; then - { { ac_try="$ac_link" -case "(($ac_try" in - *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; - *) ac_try_echo=$ac_try;; -esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_link") 2>&5 - ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; } - if { ac_try='./conftest$ac_cv_exeext' - { { case "(($ac_try" in + if { ac_try='./$ac_file' + { (case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 (eval "$ac_try") 2>&5 ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; }; then + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then cross_compiling=no else if test "$cross_compiling" = maybe; then cross_compiling=yes else - { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "cannot run C compiled programs. +{ { $as_echo "$as_me:$LINENO: error: cannot run C compiled programs. If you meant to cross compile, use \`--host'. -See \`config.log' for more details" "$LINENO" 5 ; } +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot run C compiled programs. +If you meant to cross compile, use \`--host'. +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } fi fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $cross_compiling" >&5 -$as_echo "$cross_compiling" >&6; } +{ $as_echo "$as_me:$LINENO: result: yes" >&5 +$as_echo "yes" >&6; } -rm -f conftest.$ac_ext conftest$ac_cv_exeext conftest.out +rm -f -r a.out a.out.dSYM a.exe conftest$ac_cv_exeext b.out ac_clean_files=$ac_clean_files_save -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for suffix of object files" >&5 +# Check that the compiler produces executables we can run. If not, either +# the compiler is broken, or we cross compile. +{ $as_echo "$as_me:$LINENO: checking whether we are cross compiling" >&5 +$as_echo_n "checking whether we are cross compiling... " >&6; } +{ $as_echo "$as_me:$LINENO: result: $cross_compiling" >&5 +$as_echo "$cross_compiling" >&6; } + +{ $as_echo "$as_me:$LINENO: checking for suffix of executables" >&5 +$as_echo_n "checking for suffix of executables... " >&6; } +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then + # If both `conftest.exe' and `conftest' are `present' (well, observable) +# catch `conftest.exe'. For instance with Cygwin, `ls conftest' will +# work properly (i.e., refer to `conftest.exe'), while it won't with +# `rm'. +for ac_file in conftest.exe conftest conftest.*; do + test -f "$ac_file" || continue + case $ac_file in + *.$ac_ext | *.xcoff | *.tds | *.d | *.pdb | *.xSYM | *.bb | *.bbg | *.map | *.inf | *.dSYM | *.o | *.obj ) ;; + *.* ) ac_cv_exeext=`expr "$ac_file" : '[^.]*\(\..*\)'` + break;; + * ) break;; + esac +done +else + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 +$as_echo "$as_me: error: in \`$ac_pwd':" >&2;} +{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute suffix of executables: cannot compile and link +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } +fi + +rm -f conftest$ac_cv_exeext +{ $as_echo "$as_me:$LINENO: result: $ac_cv_exeext" >&5 +$as_echo "$ac_cv_exeext" >&6; } + +rm -f conftest.$ac_ext +EXEEXT=$ac_cv_exeext +ac_exeext=$EXEEXT +{ $as_echo "$as_me:$LINENO: checking for suffix of object files" >&5 $as_echo_n "checking for suffix of object files... " >&6; } -if test "${ac_cv_objext+set}" = set; then : +if test "${ac_cv_objext+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3230,17 +2902,17 @@ main () } _ACEOF rm -f conftest.o conftest.obj -if { { ac_try="$ac_compile" +if { (ac_try="$ac_compile" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 (eval "$ac_compile") 2>&5 ac_status=$? - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; }; then : + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; then for ac_file in conftest.o conftest.obj conftest.*; do test -f "$ac_file" || continue; case $ac_file in @@ -3253,23 +2925,31 @@ else $as_echo "$as_me: failed program was:" >&5 sed 's/^/| /' conftest.$ac_ext >&5 -{ { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 +{ { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "cannot compute suffix of object files: cannot compile -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: cannot compute suffix of object files: cannot compile +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } fi + rm -f conftest.$ac_cv_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_objext" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_objext" >&5 $as_echo "$ac_cv_objext" >&6; } OBJEXT=$ac_cv_objext ac_objext=$OBJEXT -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C compiler" >&5 +{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C compiler" >&5 $as_echo_n "checking whether we are using the GNU C compiler... " >&6; } -if test "${ac_cv_c_compiler_gnu+set}" = set; then : +if test "${ac_cv_c_compiler_gnu+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3283,16 +2963,37 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_compiler_gnu=yes else - ac_compiler_gnu=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_compiler_gnu=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_c_compiler_gnu=$ac_compiler_gnu fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_compiler_gnu" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_compiler_gnu" >&5 $as_echo "$ac_cv_c_compiler_gnu" >&6; } if test $ac_compiler_gnu = yes; then GCC=yes @@ -3301,16 +3002,20 @@ else fi ac_test_CFLAGS=${CFLAGS+set} ac_save_CFLAGS=$CFLAGS -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CC accepts -g" >&5 +{ $as_echo "$as_me:$LINENO: checking whether $CC accepts -g" >&5 $as_echo_n "checking whether $CC accepts -g... " >&6; } -if test "${ac_cv_prog_cc_g+set}" = set; then : +if test "${ac_cv_prog_cc_g+set}" = set; then $as_echo_n "(cached) " >&6 else ac_save_c_werror_flag=$ac_c_werror_flag ac_c_werror_flag=yes ac_cv_prog_cc_g=no CFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3321,11 +3026,35 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cc_g=yes else - CFLAGS="" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + CFLAGS="" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3336,12 +3065,36 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : else - ac_c_werror_flag=$ac_save_c_werror_flag + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_c_werror_flag=$ac_save_c_werror_flag CFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3352,17 +3105,42 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cc_g=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_c_werror_flag=$ac_save_c_werror_flag fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_g" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_g" >&5 $as_echo "$ac_cv_prog_cc_g" >&6; } if test "$ac_test_CFLAGS" = set; then CFLAGS=$ac_save_CFLAGS @@ -3379,14 +3157,18 @@ else CFLAGS= fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to accept ISO C89" >&5 +{ $as_echo "$as_me:$LINENO: checking for $CC option to accept ISO C89" >&5 $as_echo_n "checking for $CC option to accept ISO C89... " >&6; } -if test "${ac_cv_prog_cc_c89+set}" = set; then : +if test "${ac_cv_prog_cc_c89+set}" = set; then $as_echo_n "(cached) " >&6 else ac_cv_prog_cc_c89=no ac_save_CC=$CC -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -3443,9 +3225,32 @@ for ac_arg in '' -qlanglvl=extc89 -qlanglvl=ansi -std \ -Ae "-Aa -D_HPUX_SOURCE" "-Xc -D__EXTENSIONS__" do CC="$ac_save_CC $ac_arg" - if ac_fn_c_try_compile "$LINENO"; then : + rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cc_c89=$ac_arg +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext test "x$ac_cv_prog_cc_c89" != "xno" && break done @@ -3456,19 +3261,17 @@ fi # AC_CACHE_VAL case "x$ac_cv_prog_cc_c89" in x) - { $as_echo "$as_me:${as_lineno-$LINENO}: result: none needed" >&5 + { $as_echo "$as_me:$LINENO: result: none needed" >&5 $as_echo "none needed" >&6; } ;; xno) - { $as_echo "$as_me:${as_lineno-$LINENO}: result: unsupported" >&5 + { $as_echo "$as_me:$LINENO: result: unsupported" >&5 $as_echo "unsupported" >&6; } ;; *) CC="$CC $ac_cv_prog_cc_c89" - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cc_c89" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cc_c89" >&5 $as_echo "$ac_cv_prog_cc_c89" >&6; } ;; esac -if test "x$ac_cv_prog_cc_c89" != xno; then : -fi ac_ext=c ac_cpp='$CPP $CPPFLAGS' @@ -3487,7 +3290,7 @@ am__doit: .PHONY: am__doit END # If we don't find an include directive, just comment out the code. -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for style of include used by $am_make" >&5 +{ $as_echo "$as_me:$LINENO: checking for style of include used by $am_make" >&5 $as_echo_n "checking for style of include used by $am_make... " >&6; } am__include="#" am__quote= @@ -3515,12 +3318,12 @@ if test "$am__include" = "#"; then fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $_am_result" >&5 +{ $as_echo "$as_me:$LINENO: result: $_am_result" >&5 $as_echo "$_am_result" >&6; } rm -f confinc confmf # Check whether --enable-dependency-tracking was given. -if test "${enable_dependency_tracking+set}" = set; then : +if test "${enable_dependency_tracking+set}" = set; then enableval=$enable_dependency_tracking; fi @@ -3540,9 +3343,9 @@ fi depcc="$CC" am_compiler_list= -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5 +{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 $as_echo_n "checking dependency style of $depcc... " >&6; } -if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then : +if test "${am_cv_CC_dependencies_compiler_type+set}" = set; then $as_echo_n "(cached) " >&6 else if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then @@ -3650,7 +3453,7 @@ else fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CC_dependencies_compiler_type" >&5 +{ $as_echo "$as_me:$LINENO: result: $am_cv_CC_dependencies_compiler_type" >&5 $as_echo "$am_cv_CC_dependencies_compiler_type" >&6; } CCDEPMODE=depmode=$am_cv_CC_dependencies_compiler_type @@ -3679,9 +3482,9 @@ if test -z "$CXX"; then do # Extract the first word of "$ac_tool_prefix$ac_prog", so it can be a program name with args. set dummy $ac_tool_prefix$ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_CXX+set}" = set; then : +if test "${ac_cv_prog_CXX+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$CXX"; then @@ -3692,24 +3495,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_CXX="$ac_tool_prefix$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi CXX=$ac_cv_prog_CXX if test -n "$CXX"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $CXX" >&5 + { $as_echo "$as_me:$LINENO: result: $CXX" >&5 $as_echo "$CXX" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -3723,9 +3526,9 @@ if test -z "$CXX"; then do # Extract the first word of "$ac_prog", so it can be a program name with args. set dummy $ac_prog; ac_word=$2 -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for $ac_word" >&5 +{ $as_echo "$as_me:$LINENO: checking for $ac_word" >&5 $as_echo_n "checking for $ac_word... " >&6; } -if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then : +if test "${ac_cv_prog_ac_ct_CXX+set}" = set; then $as_echo_n "(cached) " >&6 else if test -n "$ac_ct_CXX"; then @@ -3736,24 +3539,24 @@ for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_exec_ext in '' $ac_executable_extensions; do + for ac_exec_ext in '' $ac_executable_extensions; do if { test -f "$as_dir/$ac_word$ac_exec_ext" && $as_test_x "$as_dir/$ac_word$ac_exec_ext"; }; then ac_cv_prog_ac_ct_CXX="$ac_prog" - $as_echo "$as_me:${as_lineno-$LINENO}: found $as_dir/$ac_word$ac_exec_ext" >&5 + $as_echo "$as_me:$LINENO: found $as_dir/$ac_word$ac_exec_ext" >&5 break 2 fi done - done +done IFS=$as_save_IFS fi fi ac_ct_CXX=$ac_cv_prog_ac_ct_CXX if test -n "$ac_ct_CXX"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_ct_CXX" >&5 + { $as_echo "$as_me:$LINENO: result: $ac_ct_CXX" >&5 $as_echo "$ac_ct_CXX" >&6; } else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } fi @@ -3766,7 +3569,7 @@ done else case $cross_compiling:$ac_tool_warned in yes:) -{ $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: using cross tools not prefixed with host triplet" >&5 +{ $as_echo "$as_me:$LINENO: WARNING: using cross tools not prefixed with host triplet" >&5 $as_echo "$as_me: WARNING: using cross tools not prefixed with host triplet" >&2;} ac_tool_warned=yes ;; esac @@ -3777,36 +3580,53 @@ fi fi fi # Provide some information about the compiler. -$as_echo "$as_me:${as_lineno-$LINENO}: checking for C++ compiler version" >&5 +$as_echo "$as_me:$LINENO: checking for C++ compiler version" >&5 set X $ac_compile ac_compiler=$2 -for ac_option in --version -v -V -qversion; do - { { ac_try="$ac_compiler $ac_option >&5" +{ (ac_try="$ac_compiler --version >&5" case "(($ac_try" in *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; *) ac_try_echo=$ac_try;; esac -eval ac_try_echo="\"\$as_me:${as_lineno-$LINENO}: $ac_try_echo\"" -$as_echo "$ac_try_echo"; } >&5 - (eval "$ac_compiler $ac_option >&5") 2>conftest.err +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler --version >&5") 2>&5 ac_status=$? - if test -s conftest.err; then - sed '10a\ -... rest of stderr output deleted ... - 10q' conftest.err >conftest.er1 - cat conftest.er1 >&5 - fi - rm -f conftest.er1 conftest.err - $as_echo "$as_me:${as_lineno-$LINENO}: \$? = $ac_status" >&5 - test $ac_status = 0; } -done + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -v >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -v >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } +{ (ac_try="$ac_compiler -V >&5" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compiler -V >&5") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether we are using the GNU C++ compiler" >&5 +{ $as_echo "$as_me:$LINENO: checking whether we are using the GNU C++ compiler" >&5 $as_echo_n "checking whether we are using the GNU C++ compiler... " >&6; } -if test "${ac_cv_cxx_compiler_gnu+set}" = set; then : +if test "${ac_cv_cxx_compiler_gnu+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3820,16 +3640,37 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_compiler_gnu=yes else - ac_compiler_gnu=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_compiler_gnu=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cv_cxx_compiler_gnu=$ac_compiler_gnu fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_cxx_compiler_gnu" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_cxx_compiler_gnu" >&5 $as_echo "$ac_cv_cxx_compiler_gnu" >&6; } if test $ac_compiler_gnu = yes; then GXX=yes @@ -3838,16 +3679,20 @@ else fi ac_test_CXXFLAGS=${CXXFLAGS+set} ac_save_CXXFLAGS=$CXXFLAGS -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether $CXX accepts -g" >&5 +{ $as_echo "$as_me:$LINENO: checking whether $CXX accepts -g" >&5 $as_echo_n "checking whether $CXX accepts -g... " >&6; } -if test "${ac_cv_prog_cxx_g+set}" = set; then : +if test "${ac_cv_prog_cxx_g+set}" = set; then $as_echo_n "(cached) " >&6 else ac_save_cxx_werror_flag=$ac_cxx_werror_flag ac_cxx_werror_flag=yes ac_cv_prog_cxx_g=no CXXFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3858,11 +3703,35 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cxx_g=yes else - CXXFLAGS="" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + CXXFLAGS="" + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3873,12 +3742,36 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : - +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : else - ac_cxx_werror_flag=$ac_save_cxx_werror_flag + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cxx_werror_flag=$ac_save_cxx_werror_flag CXXFLAGS="-g" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -3889,17 +3782,42 @@ main () return 0; } _ACEOF -if ac_fn_cxx_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_cxx_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_prog_cxx_g=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext ac_cxx_werror_flag=$ac_save_cxx_werror_flag fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_cxx_g" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_cxx_g" >&5 $as_echo "$ac_cv_prog_cxx_g" >&6; } if test "$ac_test_CXXFLAGS" = set; then CXXFLAGS=$ac_save_CXXFLAGS @@ -3924,9 +3842,9 @@ ac_compiler_gnu=$ac_cv_c_compiler_gnu depcc="$CXX" am_compiler_list= -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking dependency style of $depcc" >&5 +{ $as_echo "$as_me:$LINENO: checking dependency style of $depcc" >&5 $as_echo_n "checking dependency style of $depcc... " >&6; } -if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then : +if test "${am_cv_CXX_dependencies_compiler_type+set}" = set; then $as_echo_n "(cached) " >&6 else if test -z "$AMDEP_TRUE" && test -f "$am_depcomp"; then @@ -4034,7 +3952,7 @@ else fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $am_cv_CXX_dependencies_compiler_type" >&5 +{ $as_echo "$as_me:$LINENO: result: $am_cv_CXX_dependencies_compiler_type" >&5 $as_echo "$am_cv_CXX_dependencies_compiler_type" >&6; } CXXDEPMODE=depmode=$am_cv_CXX_dependencies_compiler_type @@ -4049,25 +3967,116 @@ else fi -#AC_PROG_LIBTOOL +#AC_PROG_LIBTOOL +# Find a good install program. We prefer a C program (faster), +# so one script is as good as another. But avoid the broken or +# incompatible versions: +# SysV /etc/install, /usr/sbin/install +# SunOS /usr/etc/install +# IRIX /sbin/install +# AIX /bin/install +# AmigaOS /C/install, which installs bootblocks on floppy discs +# AIX 4 /usr/bin/installbsd, which doesn't work without a -g flag +# AFS /usr/afsws/bin/install, which mishandles nonexistent args +# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff" +# OS/2's system install, which has a completely different semantic +# ./install, which can be erroneously created by make from ./install.sh. +# Reject install programs that cannot install multiple files. +{ $as_echo "$as_me:$LINENO: checking for a BSD-compatible install" >&5 +$as_echo_n "checking for a BSD-compatible install... " >&6; } +if test -z "$INSTALL"; then +if test "${ac_cv_path_install+set}" = set; then + $as_echo_n "(cached) " >&6 +else + as_save_IFS=$IFS; IFS=$PATH_SEPARATOR +for as_dir in $PATH +do + IFS=$as_save_IFS + test -z "$as_dir" && as_dir=. + # Account for people who put trailing slashes in PATH elements. +case $as_dir/ in + ./ | .// | /cC/* | \ + /etc/* | /usr/sbin/* | /usr/etc/* | /sbin/* | /usr/afsws/bin/* | \ + ?:\\/os2\\/install\\/* | ?:\\/OS2\\/INSTALL\\/* | \ + /usr/ucb/* ) ;; + *) + # OSF1 and SCO ODT 3.0 have their own names for install. + # Don't use installbsd from OSF since it installs stuff as root + # by default. + for ac_prog in ginstall scoinst install; do + for ac_exec_ext in '' $ac_executable_extensions; do + if { test -f "$as_dir/$ac_prog$ac_exec_ext" && $as_test_x "$as_dir/$ac_prog$ac_exec_ext"; }; then + if test $ac_prog = install && + grep dspmsg "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # AIX install. It has an incompatible calling convention. + : + elif test $ac_prog = install && + grep pwplus "$as_dir/$ac_prog$ac_exec_ext" >/dev/null 2>&1; then + # program-specific install script used by HP pwplus--don't use. + : + else + rm -rf conftest.one conftest.two conftest.dir + echo one > conftest.one + echo two > conftest.two + mkdir conftest.dir + if "$as_dir/$ac_prog$ac_exec_ext" -c conftest.one conftest.two "`pwd`/conftest.dir" && + test -s conftest.one && test -s conftest.two && + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then + ac_cv_path_install="$as_dir/$ac_prog$ac_exec_ext -c" + break 3 + fi + fi + fi + done + done + ;; +esac + +done +IFS=$as_save_IFS + +rm -rf conftest.one conftest.two conftest.dir + +fi + if test "${ac_cv_path_install+set}" = set; then + INSTALL=$ac_cv_path_install + else + # As a last resort, use the slow shell script. Don't cache a + # value for INSTALL within a source directory, because that will + # break other packages using the cache if that directory is + # removed, or if the value is a relative name. + INSTALL=$ac_install_sh + fi +fi +{ $as_echo "$as_me:$LINENO: result: $INSTALL" >&5 +$as_echo "$INSTALL" >&6; } + +# Use test -z because SunOS4 sh mishandles braces in ${var-val}. +# It thinks the first close brace ends the variable substitution. +test -z "$INSTALL_PROGRAM" && INSTALL_PROGRAM='${INSTALL}' + +test -z "$INSTALL_SCRIPT" && INSTALL_SCRIPT='${INSTALL}' + +test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644' OPENMP_CFLAGS= # Check whether --enable-openmp was given. -if test "${enable_openmp+set}" = set; then : +if test "${enable_openmp+set}" = set; then enableval=$enable_openmp; fi if test "$enable_openmp" != no; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for $CC option to support OpenMP" >&5 + { $as_echo "$as_me:$LINENO: checking for $CC option to support OpenMP" >&5 $as_echo_n "checking for $CC option to support OpenMP... " >&6; } -if test "${ac_cv_prog_c_openmp+set}" = set; then : +if test "${ac_cv_prog_c_openmp+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ + cat >conftest.$ac_ext <<_ACEOF #ifndef _OPENMP choke me @@ -4076,15 +4085,37 @@ else int main () { return omp_get_num_threads (); } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_prog_c_openmp='none needed' else - ac_cv_prog_c_openmp='unsupported' + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_prog_c_openmp='unsupported' for ac_option in -fopenmp -xopenmp -openmp -mp -omp -qsmp=omp; do ac_save_CFLAGS=$CFLAGS CFLAGS="$CFLAGS $ac_option" - cat confdefs.h - <<_ACEOF >conftest.$ac_ext -/* end confdefs.h. */ + cat >conftest.$ac_ext <<_ACEOF #ifndef _OPENMP choke me @@ -4093,27 +4124,56 @@ else int main () { return omp_get_num_threads (); } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_prog_c_openmp=$ac_option +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext CFLAGS=$ac_save_CFLAGS if test "$ac_cv_prog_c_openmp" != unsupported; then break fi done fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_prog_c_openmp" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_prog_c_openmp" >&5 $as_echo "$ac_cv_prog_c_openmp" >&6; } case $ac_cv_prog_c_openmp in #( "none needed" | unsupported) - ;; #( + ;; #( *) - OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;; + OPENMP_CFLAGS=$ac_cv_prog_c_openmp ;; esac fi @@ -4121,14 +4181,18 @@ $as_echo "$ac_cv_prog_c_openmp" >&6; } #AC_DEFINE([_RAND],[],[RNG library to use]) -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for log2 in -lm" >&5 +{ $as_echo "$as_me:$LINENO: checking for log2 in -lm" >&5 $as_echo_n "checking for log2 in -lm... " >&6; } -if test "${ac_cv_lib_m_log2+set}" = set; then : +if test "${ac_cv_lib_m_log2+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lm $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -4146,20 +4210,47 @@ return log2 (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_m_log2=yes else - ac_cv_lib_m_log2=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_m_log2=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_m_log2" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_m_log2" >&5 $as_echo "$ac_cv_lib_m_log2" >&6; } -if test "x$ac_cv_lib_m_log2" = x""yes; then : +if test "x$ac_cv_lib_m_log2" = x""yes; then -$as_echo "#define HAVE_LOG2 /**/" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define HAVE_LOG2 /**/ +_ACEOF fi @@ -4169,14 +4260,14 @@ ac_cpp='$CPP $CPPFLAGS' ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5' ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5' ac_compiler_gnu=$ac_cv_c_compiler_gnu -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking how to run the C preprocessor" >&5 +{ $as_echo "$as_me:$LINENO: checking how to run the C preprocessor" >&5 $as_echo_n "checking how to run the C preprocessor... " >&6; } # On Suns, sometimes $CPP names a directory. if test -n "$CPP" && test -d "$CPP"; then CPP= fi if test -z "$CPP"; then - if test "${ac_cv_prog_CPP+set}" = set; then : + if test "${ac_cv_prog_CPP+set}" = set; then $as_echo_n "(cached) " >&6 else # Double quotes because CPP needs to be expanded @@ -4191,7 +4282,11 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifdef __STDC__ # include @@ -4200,34 +4295,78 @@ do #endif Syntax error _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : - +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + : else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Broken: fails on valid input. continue fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then # Broken: success on invalid input. continue else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Passes both tests. ac_preproc_ok=: break fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.i conftest.err conftest.$ac_ext -if $ac_preproc_ok; then : +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then break fi @@ -4239,7 +4378,7 @@ fi else ac_cv_prog_CPP=$CPP fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $CPP" >&5 +{ $as_echo "$as_me:$LINENO: result: $CPP" >&5 $as_echo "$CPP" >&6; } ac_preproc_ok=false for ac_c_preproc_warn_flag in '' yes @@ -4250,7 +4389,11 @@ do # exists even on freestanding compilers. # On the NeXT, cc -E runs the code through the compiler's parser, # not just through cpp. "Syntax error" is here to catch this case. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifdef __STDC__ # include @@ -4259,40 +4402,87 @@ do #endif Syntax error _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : - +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + : else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Broken: fails on valid input. continue fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext # OK, works on sane cases. Now check whether nonexistent headers # can be detected and how. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF -if ac_fn_c_try_cpp "$LINENO"; then : +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then # Broken: success on invalid input. continue else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + # Passes both tests. ac_preproc_ok=: break fi -rm -f conftest.err conftest.i conftest.$ac_ext + +rm -f conftest.err conftest.$ac_ext done # Because of `break', _AC_PREPROC_IFELSE's cleaning code was skipped. -rm -f conftest.i conftest.err conftest.$ac_ext -if $ac_preproc_ok; then : - +rm -f conftest.err conftest.$ac_ext +if $ac_preproc_ok; then + : else - { { $as_echo "$as_me:${as_lineno-$LINENO}: error: in \`$ac_pwd':" >&5 + { { $as_echo "$as_me:$LINENO: error: in \`$ac_pwd':" >&5 $as_echo "$as_me: error: in \`$ac_pwd':" >&2;} -as_fn_error $? "C preprocessor \"$CPP\" fails sanity check -See \`config.log' for more details" "$LINENO" 5 ; } +{ { $as_echo "$as_me:$LINENO: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&5 +$as_echo "$as_me: error: C preprocessor \"$CPP\" fails sanity check +See \`config.log' for more details." >&2;} + { (exit 1); exit 1; }; }; } fi ac_ext=c @@ -4302,9 +4492,9 @@ ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $ ac_compiler_gnu=$ac_cv_c_compiler_gnu -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for grep that handles long lines and -e" >&5 +{ $as_echo "$as_me:$LINENO: checking for grep that handles long lines and -e" >&5 $as_echo_n "checking for grep that handles long lines and -e... " >&6; } -if test "${ac_cv_path_GREP+set}" = set; then : +if test "${ac_cv_path_GREP+set}" = set; then $as_echo_n "(cached) " >&6 else if test -z "$GREP"; then @@ -4315,7 +4505,7 @@ for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_prog in grep ggrep; do + for ac_prog in grep ggrep; do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_GREP="$as_dir/$ac_prog$ac_exec_ext" { test -f "$ac_path_GREP" && $as_test_x "$ac_path_GREP"; } || continue @@ -4335,7 +4525,7 @@ case `"$ac_path_GREP" --version 2>&1` in $as_echo 'GREP' >> "conftest.nl" "$ac_path_GREP" -e 'GREP$' -e '-(cannot match)-' < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break - as_fn_arith $ac_count + 1 && ac_count=$as_val + ac_count=`expr $ac_count + 1` if test $ac_count -gt ${ac_path_GREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_GREP="$ac_path_GREP" @@ -4350,24 +4540,26 @@ esac $ac_path_GREP_found && break 3 done done - done +done IFS=$as_save_IFS if test -z "$ac_cv_path_GREP"; then - as_fn_error $? "no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 +$as_echo "$as_me: error: no acceptable grep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} + { (exit 1); exit 1; }; } fi else ac_cv_path_GREP=$GREP fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_GREP" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_GREP" >&5 $as_echo "$ac_cv_path_GREP" >&6; } GREP="$ac_cv_path_GREP" -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for egrep" >&5 +{ $as_echo "$as_me:$LINENO: checking for egrep" >&5 $as_echo_n "checking for egrep... " >&6; } -if test "${ac_cv_path_EGREP+set}" = set; then : +if test "${ac_cv_path_EGREP+set}" = set; then $as_echo_n "(cached) " >&6 else if echo a | $GREP -E '(a|b)' >/dev/null 2>&1 @@ -4381,7 +4573,7 @@ for as_dir in $PATH$PATH_SEPARATOR/usr/xpg4/bin do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - for ac_prog in egrep; do + for ac_prog in egrep; do for ac_exec_ext in '' $ac_executable_extensions; do ac_path_EGREP="$as_dir/$ac_prog$ac_exec_ext" { test -f "$ac_path_EGREP" && $as_test_x "$ac_path_EGREP"; } || continue @@ -4401,7 +4593,7 @@ case `"$ac_path_EGREP" --version 2>&1` in $as_echo 'EGREP' >> "conftest.nl" "$ac_path_EGREP" 'EGREP$' < "conftest.nl" >"conftest.out" 2>/dev/null || break diff "conftest.out" "conftest.nl" >/dev/null 2>&1 || break - as_fn_arith $ac_count + 1 && ac_count=$as_val + ac_count=`expr $ac_count + 1` if test $ac_count -gt ${ac_path_EGREP_max-0}; then # Best one so far, save it but keep looking for a better one ac_cv_path_EGREP="$ac_path_EGREP" @@ -4416,10 +4608,12 @@ esac $ac_path_EGREP_found && break 3 done done - done +done IFS=$as_save_IFS if test -z "$ac_cv_path_EGREP"; then - as_fn_error $? "no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&5 +$as_echo "$as_me: error: no acceptable egrep could be found in $PATH$PATH_SEPARATOR/usr/xpg4/bin" >&2;} + { (exit 1); exit 1; }; } fi else ac_cv_path_EGREP=$EGREP @@ -4427,17 +4621,21 @@ fi fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_path_EGREP" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_path_EGREP" >&5 $as_echo "$ac_cv_path_EGREP" >&6; } EGREP="$ac_cv_path_EGREP" -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for ANSI C header files" >&5 +{ $as_echo "$as_me:$LINENO: checking for ANSI C header files" >&5 $as_echo_n "checking for ANSI C header files... " >&6; } -if test "${ac_cv_header_stdc+set}" = set; then : +if test "${ac_cv_header_stdc+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4452,23 +4650,48 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_header_stdc=yes else - ac_cv_header_stdc=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_header_stdc=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext if test $ac_cv_header_stdc = yes; then # SunOS 4.x string.h does not declare mem*, contrary to ANSI. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "memchr" >/dev/null 2>&1; then : - + $EGREP "memchr" >/dev/null 2>&1; then + : else ac_cv_header_stdc=no fi @@ -4478,14 +4701,18 @@ fi if test $ac_cv_header_stdc = yes; then # ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI. - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include _ACEOF if (eval "$ac_cpp conftest.$ac_ext") 2>&5 | - $EGREP "free" >/dev/null 2>&1; then : - + $EGREP "free" >/dev/null 2>&1; then + : else ac_cv_header_stdc=no fi @@ -4495,10 +4722,14 @@ fi if test $ac_cv_header_stdc = yes; then # /bin/cc in Irix-4.0.5 gets non-ANSI ctype macros unless using -ansi. - if test "$cross_compiling" = yes; then : + if test "$cross_compiling" = yes; then : else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4525,49 +4756,269 @@ main () return 0; } _ACEOF -if ac_fn_c_try_run "$LINENO"; then : - +rm -f conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { ac_try='./conftest$ac_exeext' + { (case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_try") 2>&5 + ac_status=$? + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); }; }; then + : else - ac_cv_header_stdc=no + $as_echo "$as_me: program exited with status $ac_status" >&5 +$as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + +( exit $ac_status ) +ac_cv_header_stdc=no fi -rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext \ - conftest.$ac_objext conftest.beam conftest.$ac_ext +rm -rf conftest.dSYM +rm -f core *.core core.conftest.* gmon.out bb.out conftest$ac_exeext conftest.$ac_objext conftest.$ac_ext fi + fi fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_stdc" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_stdc" >&5 $as_echo "$ac_cv_header_stdc" >&6; } if test $ac_cv_header_stdc = yes; then -$as_echo "#define STDC_HEADERS 1" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define STDC_HEADERS 1 +_ACEOF fi #AC_CHECK_HEADERS(sys/resource.h) #AC_CHECK_HEADERS(getopt.h) # On IRIX 5.3, sys/types and inttypes.h are conflicting. + + + + + + + + + for ac_header in sys/types.h sys/stat.h stdlib.h string.h memory.h strings.h \ inttypes.h stdint.h unistd.h -do : - as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` -ac_fn_c_check_header_compile "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default -" -if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : +do +as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default + +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + eval "$as_ac_Header=yes" +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + eval "$as_ac_Header=no" +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF fi - -done - - -for ac_header in stdlib.h string.h sys/time.h -do : - as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` -ac_fn_c_check_header_mongrel "$LINENO" "$ac_header" "$as_ac_Header" "$ac_includes_default" -if eval test \"x\$"$as_ac_Header"\" = x"yes"; then : + +done + + + + + +for ac_header in stdlib.h string.h sys/time.h +do +as_ac_Header=`$as_echo "ac_cv_header_$ac_header" | $as_tr_sh` +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + { $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +else + # Is the header compilable? +{ $as_echo "$as_me:$LINENO: checking $ac_header usability" >&5 +$as_echo_n "checking $ac_header usability... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +#include <$ac_header> +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + ac_header_compiler=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_compiler=no +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_compiler" >&5 +$as_echo "$ac_header_compiler" >&6; } + +# Is the header present? +{ $as_echo "$as_me:$LINENO: checking $ac_header presence" >&5 +$as_echo_n "checking $ac_header presence... " >&6; } +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +#include <$ac_header> +_ACEOF +if { (ac_try="$ac_cpp conftest.$ac_ext" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_cpp conftest.$ac_ext") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } >/dev/null && { + test -z "$ac_c_preproc_warn_flag$ac_c_werror_flag" || + test ! -s conftest.err + }; then + ac_header_preproc=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_header_preproc=no +fi + +rm -f conftest.err conftest.$ac_ext +{ $as_echo "$as_me:$LINENO: result: $ac_header_preproc" >&5 +$as_echo "$ac_header_preproc" >&6; } + +# So? What about this header? +case $ac_header_compiler:$ac_header_preproc:$ac_c_preproc_warn_flag in + yes:no: ) + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&5 +$as_echo "$as_me: WARNING: $ac_header: accepted by the compiler, rejected by the preprocessor!" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the compiler's result" >&5 +$as_echo "$as_me: WARNING: $ac_header: proceeding with the compiler's result" >&2;} + ac_header_preproc=yes + ;; + no:yes:* ) + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: present but cannot be compiled" >&5 +$as_echo "$as_me: WARNING: $ac_header: present but cannot be compiled" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: check for missing prerequisite headers?" >&5 +$as_echo "$as_me: WARNING: $ac_header: check for missing prerequisite headers?" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: see the Autoconf documentation" >&5 +$as_echo "$as_me: WARNING: $ac_header: see the Autoconf documentation" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&5 +$as_echo "$as_me: WARNING: $ac_header: section \"Present But Cannot Be Compiled\"" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: proceeding with the preprocessor's result" >&5 +$as_echo "$as_me: WARNING: $ac_header: proceeding with the preprocessor's result" >&2;} + { $as_echo "$as_me:$LINENO: WARNING: $ac_header: in the future, the compiler will take precedence" >&5 +$as_echo "$as_me: WARNING: $ac_header: in the future, the compiler will take precedence" >&2;} + + ;; +esac +{ $as_echo "$as_me:$LINENO: checking for $ac_header" >&5 +$as_echo_n "checking for $ac_header... " >&6; } +if { as_var=$as_ac_Header; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + eval "$as_ac_Header=\$ac_header_preproc" +fi +ac_res=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } + +fi +as_val=`eval 'as_val=${'$as_ac_Header'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_header" | $as_tr_cpp` 1 _ACEOF @@ -4577,12 +5028,16 @@ fi done -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for an ANSI C-conforming const" >&5 +{ $as_echo "$as_me:$LINENO: checking for an ANSI C-conforming const" >&5 $as_echo_n "checking for an ANSI C-conforming const... " >&6; } -if test "${ac_cv_c_const+set}" = set; then : +if test "${ac_cv_c_const+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4642,29 +5097,56 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_c_const=yes else - ac_cv_c_const=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_c_const=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_const" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_const" >&5 $as_echo "$ac_cv_c_const" >&6; } if test $ac_cv_c_const = no; then -$as_echo "#define const /**/" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define const /**/ +_ACEOF fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for inline" >&5 +{ $as_echo "$as_me:$LINENO: checking for inline" >&5 $as_echo_n "checking for inline... " >&6; } -if test "${ac_cv_c_inline+set}" = set; then : +if test "${ac_cv_c_inline+set}" = set; then $as_echo_n "(cached) " >&6 else ac_cv_c_inline=no for ac_kw in inline __inline__ __inline; do - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #ifndef __cplusplus typedef int foo_t; @@ -4673,17 +5155,41 @@ $ac_kw foo_t foo () {return 0; } #endif _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_c_inline=$ac_kw +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext test "$ac_cv_c_inline" != no && break done fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_c_inline" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_c_inline" >&5 $as_echo "$ac_cv_c_inline" >&6; } + case $ac_cv_c_inline in inline | yes) ;; *) @@ -4699,9 +5205,102 @@ _ACEOF ;; esac -ac_fn_c_check_type "$LINENO" "size_t" "ac_cv_type_size_t" "$ac_includes_default" -if test "x$ac_cv_type_size_t" = x""yes; then : +{ $as_echo "$as_me:$LINENO: checking for size_t" >&5 +$as_echo_n "checking for size_t... " >&6; } +if test "${ac_cv_type_size_t+set}" = set; then + $as_echo_n "(cached) " >&6 +else + ac_cv_type_size_t=no +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if (sizeof (size_t)) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +$ac_includes_default +int +main () +{ +if (sizeof ((size_t))) + return 0; + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + : +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_type_size_t=yes +fi + +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + +fi +rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_type_size_t" >&5 +$as_echo "$ac_cv_type_size_t" >&6; } +if test "x$ac_cv_type_size_t" = x""yes; then + : else cat >>confdefs.h <<_ACEOF @@ -4710,12 +5309,16 @@ _ACEOF fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether time.h and sys/time.h may both be included" >&5 +{ $as_echo "$as_me:$LINENO: checking whether time.h and sys/time.h may both be included" >&5 $as_echo_n "checking whether time.h and sys/time.h may both be included... " >&6; } -if test "${ac_cv_header_time+set}" = set; then : +if test "${ac_cv_header_time+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4730,27 +5333,54 @@ return 0; return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_header_time=yes else - ac_cv_header_time=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_header_time=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_header_time" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_header_time" >&5 $as_echo "$ac_cv_header_time" >&6; } if test $ac_cv_header_time = yes; then -$as_echo "#define TIME_WITH_SYS_TIME 1" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define TIME_WITH_SYS_TIME 1 +_ACEOF fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking whether struct tm is in sys/time.h or time.h" >&5 +{ $as_echo "$as_me:$LINENO: checking whether struct tm is in sys/time.h or time.h" >&5 $as_echo_n "checking whether struct tm is in sys/time.h or time.h... " >&6; } -if test "${ac_cv_struct_tm+set}" = set; then : +if test "${ac_cv_struct_tm+set}" = set; then $as_echo_n "(cached) " >&6 else - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ #include #include @@ -4765,18 +5395,41 @@ struct tm tm; return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then ac_cv_struct_tm=time.h else - ac_cv_struct_tm=sys/time.h + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_struct_tm=sys/time.h fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_struct_tm" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_struct_tm" >&5 $as_echo "$ac_cv_struct_tm" >&6; } if test $ac_cv_struct_tm = sys/time.h; then -$as_echo "#define TM_IN_SYS_TIME 1" >>confdefs.h +cat >>confdefs.h <<\_ACEOF +#define TM_IN_SYS_TIME 1 +_ACEOF fi @@ -4799,10 +5452,14 @@ if test "x$GXX" = "xyes"; then fi -If Sun cc is present, define appropriate compiler flags -{ $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun C compiler" >&5 +#If Sun cc is present, define appropriate compiler flags +{ $as_echo "$as_me:$LINENO: checking for Sun C compiler" >&5 $as_echo_n "checking for Sun C compiler... " >&6; } -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4816,22 +5473,47 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } gtfold_cv_check_sunpro_cc=yes else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } gtfold_cv_check_sunpro_cc=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext if test "$gtfold_cv_check_sunpro_cc" == "yes"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun C compiler architecture target" >&5 + { $as_echo "$as_me:$LINENO: checking for Sun C compiler architecture target" >&5 $as_echo_n "checking for Sun C compiler architecture target... " >&6; } - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4845,15 +5527,36 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } gtfold_cv_check_sun_sparc=yes else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } gtfold_cv_check_sun_sparc=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi @@ -4861,9 +5564,13 @@ if test "$gtfold_cv_check_sunpro_cc" == "yes"; then if test "$gtfold_cv_check_sun_sparc" == "yes"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for Sun sparc v9 architecture" >&5 + { $as_echo "$as_me:$LINENO: checking for Sun sparc v9 architecture" >&5 $as_echo_n "checking for Sun sparc v9 architecture... " >&6; } - cat confdefs.h - <<_ACEOF >conftest.$ac_ext + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ int @@ -4877,15 +5584,36 @@ main () return 0; } _ACEOF -if ac_fn_c_try_compile "$LINENO"; then : - { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5 +rm -f conftest.$ac_objext +if { (ac_try="$ac_compile" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_compile") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest.$ac_objext; then + { $as_echo "$as_me:$LINENO: result: yes" >&5 $as_echo "yes" >&6; } gtfold_cv_check_sun_sparcv9=yes else - { $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5 + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + { $as_echo "$as_me:$LINENO: result: no" >&5 $as_echo "no" >&6; } gtfold_cv_check_sun_sparcv9=no fi + rm -f core conftest.err conftest.$ac_objext conftest.$ac_ext fi fi @@ -4908,14 +5636,18 @@ fi if test "$enable_openmp" != 'no'; then if test "x${GCC}" = "xyes"; then - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GOMP_parallel_start in -lomp" >&5 + { $as_echo "$as_me:$LINENO: checking for GOMP_parallel_start in -lomp" >&5 $as_echo_n "checking for GOMP_parallel_start in -lomp... " >&6; } -if test "${ac_cv_lib_omp_GOMP_parallel_start+set}" = set; then : +if test "${ac_cv_lib_omp_GOMP_parallel_start+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lomp $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -4933,29 +5665,58 @@ return GOMP_parallel_start (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_omp_GOMP_parallel_start=yes else - ac_cv_lib_omp_GOMP_parallel_start=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_omp_GOMP_parallel_start=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_omp_GOMP_parallel_start" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_omp_GOMP_parallel_start" >&5 $as_echo "$ac_cv_lib_omp_GOMP_parallel_start" >&6; } -if test "x$ac_cv_lib_omp_GOMP_parallel_start" = x""yes; then : +if test "x$ac_cv_lib_omp_GOMP_parallel_start" = x""yes; then LIB_OMP="-lgomp" fi - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for GOMP_parallel_start in -lgomp" >&5 + { $as_echo "$as_me:$LINENO: checking for GOMP_parallel_start in -lgomp" >&5 $as_echo_n "checking for GOMP_parallel_start in -lgomp... " >&6; } -if test "${ac_cv_lib_gomp_GOMP_parallel_start+set}" = set; then : +if test "${ac_cv_lib_gomp_GOMP_parallel_start+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lgomp $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -4973,30 +5734,59 @@ return GOMP_parallel_start (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_gomp_GOMP_parallel_start=yes else - ac_cv_lib_gomp_GOMP_parallel_start=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_gomp_GOMP_parallel_start=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_gomp_GOMP_parallel_start" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_gomp_GOMP_parallel_start" >&5 $as_echo "$ac_cv_lib_gomp_GOMP_parallel_start" >&6; } -if test "x$ac_cv_lib_gomp_GOMP_parallel_start" = x""yes; then : +if test "x$ac_cv_lib_gomp_GOMP_parallel_start" = x""yes; then GOMP_LIBS="-lgomp" fi else - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sunw_mp_register_warn in -lmtsk" >&5 + { $as_echo "$as_me:$LINENO: checking for sunw_mp_register_warn in -lmtsk" >&5 $as_echo_n "checking for sunw_mp_register_warn in -lmtsk... " >&6; } -if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then : +if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lmtsk $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -5014,29 +5804,58 @@ return sunw_mp_register_warn (); return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then ac_cv_lib_mtsk_sunw_mp_register_warn=yes else - ac_cv_lib_mtsk_sunw_mp_register_warn=no + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_mtsk_sunw_mp_register_warn=no fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext LIBS=$ac_check_lib_save_LIBS fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 $as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; } -if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then : +if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then LIB_OMP="-lmtsk" fi - { $as_echo "$as_me:${as_lineno-$LINENO}: checking for sunw_mp_register_warn in -lmtsk" >&5 + { $as_echo "$as_me:$LINENO: checking for sunw_mp_register_warn in -lmtsk" >&5 $as_echo_n "checking for sunw_mp_register_warn in -lmtsk... " >&6; } -if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then : +if test "${ac_cv_lib_mtsk_sunw_mp_register_warn+set}" = set; then $as_echo_n "(cached) " >&6 else ac_check_lib_save_LIBS=$LIBS LIBS="-lmtsk $LIBS" -cat confdefs.h - <<_ACEOF >conftest.$ac_ext +cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF /* end confdefs.h. */ /* Override any GCC internal prototype to avoid an error. @@ -5045,40 +5864,156 @@ cat confdefs.h - <<_ACEOF >conftest.$ac_ext #ifdef __cplusplus extern "C" #endif -char sunw_mp_register_warn (); +char sunw_mp_register_warn (); +int +main () +{ +return sunw_mp_register_warn (); + ; + return 0; +} +_ACEOF +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + ac_cv_lib_mtsk_sunw_mp_register_warn=yes +else + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 + + ac_cv_lib_mtsk_sunw_mp_register_warn=no +fi + +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +LIBS=$ac_check_lib_save_LIBS +fi +{ $as_echo "$as_me:$LINENO: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 +$as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; } +if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then + GOMP_LIBS="-lmtsk" +fi + + fi + LIBS="$GOMP_LIBS $LIBS" +fi + + + + + +for ac_func in floor gettimeofday pow +do +as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` +{ $as_echo "$as_me:$LINENO: checking for $ac_func" >&5 +$as_echo_n "checking for $ac_func... " >&6; } +if { as_var=$as_ac_var; eval "test \"\${$as_var+set}\" = set"; }; then + $as_echo_n "(cached) " >&6 +else + cat >conftest.$ac_ext <<_ACEOF +/* confdefs.h. */ +_ACEOF +cat confdefs.h >>conftest.$ac_ext +cat >>conftest.$ac_ext <<_ACEOF +/* end confdefs.h. */ +/* Define $ac_func to an innocuous variant, in case declares $ac_func. + For example, HP-UX 11i declares gettimeofday. */ +#define $ac_func innocuous_$ac_func + +/* System header to define __stub macros and hopefully few prototypes, + which can conflict with char $ac_func (); below. + Prefer to if __STDC__ is defined, since + exists even on freestanding compilers. */ + +#ifdef __STDC__ +# include +#else +# include +#endif + +#undef $ac_func + +/* Override any GCC internal prototype to avoid an error. + Use char because int might match the return type of a GCC + builtin and then its argument prototype would still apply. */ +#ifdef __cplusplus +extern "C" +#endif +char $ac_func (); +/* The GNU C library defines this for functions which it implements + to always fail with ENOSYS. Some functions are actually named + something starting with __ and the normal name is an alias. */ +#if defined __stub_$ac_func || defined __stub___$ac_func +choke me +#endif + int main () { -return sunw_mp_register_warn (); +return $ac_func (); ; return 0; } _ACEOF -if ac_fn_c_try_link "$LINENO"; then : - ac_cv_lib_mtsk_sunw_mp_register_warn=yes +rm -f conftest.$ac_objext conftest$ac_exeext +if { (ac_try="$ac_link" +case "(($ac_try" in + *\"* | *\`* | *\\*) ac_try_echo=\$ac_try;; + *) ac_try_echo=$ac_try;; +esac +eval ac_try_echo="\"\$as_me:$LINENO: $ac_try_echo\"" +$as_echo "$ac_try_echo") >&5 + (eval "$ac_link") 2>conftest.er1 + ac_status=$? + grep -v '^ *+' conftest.er1 >conftest.err + rm -f conftest.er1 + cat conftest.err >&5 + $as_echo "$as_me:$LINENO: \$? = $ac_status" >&5 + (exit $ac_status); } && { + test -z "$ac_c_werror_flag" || + test ! -s conftest.err + } && test -s conftest$ac_exeext && { + test "$cross_compiling" = yes || + $as_test_x conftest$ac_exeext + }; then + eval "$as_ac_var=yes" else - ac_cv_lib_mtsk_sunw_mp_register_warn=no -fi -rm -f core conftest.err conftest.$ac_objext \ - conftest$ac_exeext conftest.$ac_ext -LIBS=$ac_check_lib_save_LIBS -fi -{ $as_echo "$as_me:${as_lineno-$LINENO}: result: $ac_cv_lib_mtsk_sunw_mp_register_warn" >&5 -$as_echo "$ac_cv_lib_mtsk_sunw_mp_register_warn" >&6; } -if test "x$ac_cv_lib_mtsk_sunw_mp_register_warn" = x""yes; then : - GOMP_LIBS="-lmtsk" -fi + $as_echo "$as_me: failed program was:" >&5 +sed 's/^/| /' conftest.$ac_ext >&5 - fi - LIBS="$GOMP_LIBS $LIBS" + eval "$as_ac_var=no" fi - -for ac_func in floor gettimeofday pow -do : - as_ac_var=`$as_echo "ac_cv_func_$ac_func" | $as_tr_sh` -ac_fn_c_check_func "$LINENO" "$ac_func" "$as_ac_var" -if eval test \"x\$"$as_ac_var"\" = x"yes"; then : +rm -rf conftest.dSYM +rm -f core conftest.err conftest.$ac_objext conftest_ipa8_conftest.oo \ + conftest$ac_exeext conftest.$ac_ext +fi +ac_res=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + { $as_echo "$as_me:$LINENO: result: $ac_res" >&5 +$as_echo "$ac_res" >&6; } +as_val=`eval 'as_val=${'$as_ac_var'} + $as_echo "$as_val"'` + if test "x$as_val" = x""yes; then cat >>confdefs.h <<_ACEOF #define `$as_echo "HAVE_$ac_func" | $as_tr_cpp` 1 _ACEOF @@ -5088,12 +6023,14 @@ done # Check whether --enable-debug was given. -if test "${enable_debug+set}" = set; then : +if test "${enable_debug+set}" = set; then enableval=$enable_debug; case "${enableval}" in "" | y | ye | yes) debug=true; CFLAGS=$(echo $CFLAGS -g | sed -e 's/-O\|-O2\|-O3//g') ;; n | no) debug=false ;; - *) as_fn_error $? "bad value ${enableval} for --enable-debug" "$LINENO" 5 ;; + *) { { $as_echo "$as_me:$LINENO: error: bad value ${enableval} for --enable-debug" >&5 +$as_echo "$as_me: error: bad value ${enableval} for --enable-debug" >&2;} + { (exit 1); exit 1; }; } ;; esac else debug=false @@ -5110,7 +6047,7 @@ fi ac_config_files="$ac_config_files Makefile src/Makefile data/Makefile include/Makefile" -ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile" +ac_config_files="$ac_config_files data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile data/RNAParams/Makefile" cat >confcache <<\_ACEOF @@ -5140,13 +6077,13 @@ _ACEOF case $ac_val in #( *${as_nl}*) case $ac_var in #( - *_cv_*) { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: cache variable $ac_var contains a newline" >&5 + *_cv_*) { $as_echo "$as_me:$LINENO: WARNING: cache variable $ac_var contains a newline" >&5 $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; esac case $ac_var in #( _ | IFS | as_nl) ;; #( BASH_ARGV | BASH_SOURCE) eval $ac_var= ;; #( - *) { eval $ac_var=; unset $ac_var;} ;; + *) $as_unset $ac_var ;; esac ;; esac done @@ -5154,8 +6091,8 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; (set) 2>&1 | case $as_nl`(ac_space=' '; set) 2>&1` in #( *${as_nl}ac_space=\ *) - # `set' does not quote correctly, so add quotes: double-quote - # substitution turns \\\\ into \\, and sed turns \\ into \. + # `set' does not quote correctly, so add quotes (double-quote + # substitution turns \\\\ into \\, and sed turns \\ into \). sed -n \ "s/'/'\\\\''/g; s/^\\([_$as_cr_alnum]*_cv_[_$as_cr_alnum]*\\)=\\(.*\\)/\\1='\\2'/p" @@ -5178,11 +6115,11 @@ $as_echo "$as_me: WARNING: cache variable $ac_var contains a newline" >&2;} ;; if diff "$cache_file" confcache >/dev/null 2>&1; then :; else if test -w "$cache_file"; then test "x$cache_file" != "x/dev/null" && - { $as_echo "$as_me:${as_lineno-$LINENO}: updating cache $cache_file" >&5 + { $as_echo "$as_me:$LINENO: updating cache $cache_file" >&5 $as_echo "$as_me: updating cache $cache_file" >&6;} cat confcache >$cache_file else - { $as_echo "$as_me:${as_lineno-$LINENO}: not updating unwritable cache $cache_file" >&5 + { $as_echo "$as_me:$LINENO: not updating unwritable cache $cache_file" >&5 $as_echo "$as_me: not updating unwritable cache $cache_file" >&6;} fi fi @@ -5196,15 +6133,14 @@ DEFS=-DHAVE_CONFIG_H ac_libobjs= ac_ltlibobjs= -U= for ac_i in : $LIBOBJS; do test "x$ac_i" = x: && continue # 1. Remove the extension, and $U if already installed. ac_script='s/\$U\././;s/\.o$//;s/\.obj$//' ac_i=`$as_echo "$ac_i" | sed "$ac_script"` # 2. Prepend LIBOBJDIR. When used with automake>=1.10 LIBOBJDIR # will be set to the directory where LIBOBJS objects are built. - as_fn_append ac_libobjs " \${LIBOBJDIR}$ac_i\$U.$ac_objext" - as_fn_append ac_ltlibobjs " \${LIBOBJDIR}$ac_i"'$U.lo' + ac_libobjs="$ac_libobjs \${LIBOBJDIR}$ac_i\$U.$ac_objext" + ac_ltlibobjs="$ac_ltlibobjs \${LIBOBJDIR}$ac_i"'$U.lo' done LIBOBJS=$ac_libobjs @@ -5220,30 +6156,41 @@ else fi if test -z "${AMDEP_TRUE}" && test -z "${AMDEP_FALSE}"; then - as_fn_error $? "conditional \"AMDEP\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"AMDEP\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"AMDEP\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi if test -z "${am__fastdepCC_TRUE}" && test -z "${am__fastdepCC_FALSE}"; then - as_fn_error $? "conditional \"am__fastdepCC\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCC\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"am__fastdepCC\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi if test -z "${am__fastdepCXX_TRUE}" && test -z "${am__fastdepCXX_FALSE}"; then - as_fn_error $? "conditional \"am__fastdepCXX\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"am__fastdepCXX\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"am__fastdepCXX\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi if test -z "${GTFOLD_DEBUG_TRUE}" && test -z "${GTFOLD_DEBUG_FALSE}"; then - as_fn_error $? "conditional \"GTFOLD_DEBUG\" was never defined. -Usually this means the macro was only invoked conditionally." "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: conditional \"GTFOLD_DEBUG\" was never defined. +Usually this means the macro was only invoked conditionally." >&5 +$as_echo "$as_me: error: conditional \"GTFOLD_DEBUG\" was never defined. +Usually this means the macro was only invoked conditionally." >&2;} + { (exit 1); exit 1; }; } fi : ${CONFIG_STATUS=./config.status} ac_write_fail=0 ac_clean_files_save=$ac_clean_files ac_clean_files="$ac_clean_files $CONFIG_STATUS" -{ $as_echo "$as_me:${as_lineno-$LINENO}: creating $CONFIG_STATUS" >&5 +{ $as_echo "$as_me:$LINENO: creating $CONFIG_STATUS" >&5 $as_echo "$as_me: creating $CONFIG_STATUS" >&6;} -as_write_fail=0 -cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 +cat >$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 #! $SHELL # Generated by $as_me. # Run this file to recreate the current configuration. @@ -5253,18 +6200,17 @@ cat >$CONFIG_STATUS <<_ASEOF || as_write_fail=1 debug=false ac_cs_recheck=false ac_cs_silent=false - SHELL=\${CONFIG_SHELL-$SHELL} -export SHELL -_ASEOF -cat >>$CONFIG_STATUS <<\_ASEOF || as_write_fail=1 -## -------------------- ## -## M4sh Initialization. ## -## -------------------- ## +_ACEOF + +cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 +## --------------------- ## +## M4sh Initialization. ## +## --------------------- ## # Be more Bourne compatible DUALCASE=1; export DUALCASE # for MKS sh -if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : +if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then emulate sh NULLCMD=: # Pre-4.2 versions of Zsh do word splitting on ${1+"$@"}, which @@ -5272,15 +6218,23 @@ if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then : alias -g '${1+"$@"}'='"$@"' setopt NO_GLOB_SUBST else - case `(set -o) 2>/dev/null` in #( - *posix*) : - set -o posix ;; #( - *) : - ;; + case `(set -o) 2>/dev/null` in + *posix*) set -o posix ;; esac + fi + + +# PATH needs CR +# Avoid depending upon Character Ranges. +as_cr_letters='abcdefghijklmnopqrstuvwxyz' +as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' +as_cr_Letters=$as_cr_letters$as_cr_LETTERS +as_cr_digits='0123456789' +as_cr_alnum=$as_cr_Letters$as_cr_digits + as_nl=' ' export as_nl @@ -5288,13 +6242,7 @@ export as_nl as_echo='\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\\' as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo as_echo=$as_echo$as_echo$as_echo$as_echo$as_echo$as_echo -# Prefer a ksh shell builtin over an external printf program on Solaris, -# but without wasting forks for bash or zsh. -if test -z "$BASH_VERSION$ZSH_VERSION" \ - && (test "X`print -r -- $as_echo`" = "X$as_echo") 2>/dev/null; then - as_echo='print -r --' - as_echo_n='print -rn --' -elif (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then +if (test "X`printf %s $as_echo`" = "X$as_echo") 2>/dev/null; then as_echo='printf %s\n' as_echo_n='printf %s' else @@ -5305,7 +6253,7 @@ else as_echo_body='eval expr "X$1" : "X\\(.*\\)"' as_echo_n_body='eval arg=$1; - case $arg in #( + case $arg in *"$as_nl"*) expr "X$arg" : "X\\(.*\\)$as_nl"; arg=`expr "X$arg" : ".*$as_nl\\(.*\\)"`;; @@ -5328,6 +6276,13 @@ if test "${PATH_SEPARATOR+set}" != set; then } fi +# Support unset when possible. +if ( (MAIL=60; unset MAIL) || exit) >/dev/null 2>&1; then + as_unset=unset +else + as_unset=false +fi + # IFS # We need space, tab and new line, in precisely that order. Quoting is @@ -5337,15 +6292,15 @@ fi IFS=" "" $as_nl" # Find who we are. Look in the path if we contain no directory separator. -case $0 in #(( +case $0 in *[\\/]* ) as_myself=$0 ;; *) as_save_IFS=$IFS; IFS=$PATH_SEPARATOR for as_dir in $PATH do IFS=$as_save_IFS test -z "$as_dir" && as_dir=. - test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break - done + test -r "$as_dir/$0" && as_myself=$as_dir/$0 && break +done IFS=$as_save_IFS ;; @@ -5357,16 +6312,12 @@ if test "x$as_myself" = x; then fi if test ! -f "$as_myself"; then $as_echo "$as_myself: error: cannot find myself; rerun with an absolute file name" >&2 - exit 1 + { (exit 1); exit 1; } fi -# Unset variables that we do not need and which cause bugs (e.g. in -# pre-3.0 UWIN ksh). But do not cause bugs in bash 2.01; the "|| exit 1" -# suppresses any "Segmentation fault" message there. '((' could -# trigger a bug in pdksh 5.2.14. -for as_var in BASH_ENV ENV MAIL MAILPATH -do eval test x\${$as_var+set} = xset \ - && ( (unset $as_var) || exit 1) >/dev/null 2>&1 && unset $as_var || : +# Work around bugs in pre-3.0 UWIN ksh. +for as_var in ENV MAIL MAILPATH +do ($as_unset $as_var) >/dev/null 2>&1 && $as_unset $as_var done PS1='$ ' PS2='> ' @@ -5378,89 +6329,7 @@ export LC_ALL LANGUAGE=C export LANGUAGE -# CDPATH. -(unset CDPATH) >/dev/null 2>&1 && unset CDPATH - - -# as_fn_error STATUS ERROR [LINENO LOG_FD] -# ---------------------------------------- -# Output "`basename $0`: error: ERROR" to stderr. If LINENO and LOG_FD are -# provided, also output the error to LOG_FD, referencing LINENO. Then exit the -# script with STATUS, using 1 if that was 0. -as_fn_error () -{ - as_status=$1; test $as_status -eq 0 && as_status=1 - if test "$4"; then - as_lineno=${as_lineno-"$3"} as_lineno_stack=as_lineno_stack=$as_lineno_stack - $as_echo "$as_me:${as_lineno-$LINENO}: error: $2" >&$4 - fi - $as_echo "$as_me: error: $2" >&2 - as_fn_exit $as_status -} # as_fn_error - - -# as_fn_set_status STATUS -# ----------------------- -# Set $? to STATUS, without forking. -as_fn_set_status () -{ - return $1 -} # as_fn_set_status - -# as_fn_exit STATUS -# ----------------- -# Exit the shell with STATUS, even in a "trap 0" or "set -e" context. -as_fn_exit () -{ - set +e - as_fn_set_status $1 - exit $1 -} # as_fn_exit - -# as_fn_unset VAR -# --------------- -# Portably unset VAR. -as_fn_unset () -{ - { eval $1=; unset $1;} -} -as_unset=as_fn_unset -# as_fn_append VAR VALUE -# ---------------------- -# Append the text in VALUE to the end of the definition contained in VAR. Take -# advantage of any shell optimizations that allow amortized linear growth over -# repeated appends, instead of the typical quadratic growth present in naive -# implementations. -if (eval "as_var=1; as_var+=2; test x\$as_var = x12") 2>/dev/null; then : - eval 'as_fn_append () - { - eval $1+=\$2 - }' -else - as_fn_append () - { - eval $1=\$$1\$2 - } -fi # as_fn_append - -# as_fn_arith ARG... -# ------------------ -# Perform arithmetic evaluation on the ARGs, and store the result in the -# global $as_val. Take advantage of shells that can avoid forks. The arguments -# must be portable across $(()) and expr. -if (eval "test \$(( 1 + 1 )) = 2") 2>/dev/null; then : - eval 'as_fn_arith () - { - as_val=$(( $* )) - }' -else - as_fn_arith () - { - as_val=`expr "$@" || test $? -eq 1` - } -fi # as_fn_arith - - +# Required to use basename. if expr a : '\(a\)' >/dev/null 2>&1 && test "X`expr 00001 : '.*\(...\)'`" = X001; then as_expr=expr @@ -5474,12 +6343,8 @@ else as_basename=false fi -if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then - as_dirname=dirname -else - as_dirname=false -fi +# Name of the executable. as_me=`$as_basename -- "$0" || $as_expr X/"$0" : '.*/\([^/][^/]*\)/*$' \| \ X"$0" : 'X\(//\)$' \| \ @@ -5499,25 +6364,76 @@ $as_echo X/"$0" | } s/.*/./; q'` -# Avoid depending upon Character Ranges. -as_cr_letters='abcdefghijklmnopqrstuvwxyz' -as_cr_LETTERS='ABCDEFGHIJKLMNOPQRSTUVWXYZ' -as_cr_Letters=$as_cr_letters$as_cr_LETTERS -as_cr_digits='0123456789' -as_cr_alnum=$as_cr_Letters$as_cr_digits +# CDPATH. +$as_unset CDPATH + + + + as_lineno_1=$LINENO + as_lineno_2=$LINENO + test "x$as_lineno_1" != "x$as_lineno_2" && + test "x`expr $as_lineno_1 + 1`" = "x$as_lineno_2" || { + + # Create $as_me.lineno as a copy of $as_myself, but with $LINENO + # uniformly replaced by the line number. The first 'sed' inserts a + # line-number line after each line using $LINENO; the second 'sed' + # does the real work. The second script uses 'N' to pair each + # line-number line with the line containing $LINENO, and appends + # trailing '-' during substitution so that $LINENO is not a special + # case at line end. + # (Raja R Harinath suggested sed '=', and Paul Eggert wrote the + # scripts with optimization help from Paolo Bonzini. Blame Lee + # E. McMahon (1931-1989) for sed's syntax. :-) + sed -n ' + p + /[$]LINENO/= + ' <$as_myself | + sed ' + s/[$]LINENO.*/&-/ + t lineno + b + :lineno + N + :loop + s/[$]LINENO\([^'$as_cr_alnum'_].*\n\)\(.*\)/\2\1\2/ + t loop + s/-\n.*// + ' >$as_me.lineno && + chmod +x "$as_me.lineno" || + { $as_echo "$as_me: error: cannot create $as_me.lineno; rerun with a POSIX shell" >&2 + { (exit 1); exit 1; }; } + + # Don't try to exec as it changes $[0], causing all sort of problems + # (the dirname of $[0] is not the place where we might find the + # original and so on. Autoconf is especially sensitive to this). + . "./$as_me.lineno" + # Exit status is that of the last command. + exit +} + + +if (as_dir=`dirname -- /` && test "X$as_dir" = X/) >/dev/null 2>&1; then + as_dirname=dirname +else + as_dirname=false +fi ECHO_C= ECHO_N= ECHO_T= -case `echo -n x` in #((((( +case `echo -n x` in -n*) - case `echo 'xy\c'` in + case `echo 'x\c'` in *c*) ECHO_T=' ';; # ECHO_T is single tab character. - xy) ECHO_C='\c';; - *) echo `echo ksh88 bug on AIX 6.1` > /dev/null - ECHO_T=' ';; + *) ECHO_C='\c';; esac;; *) ECHO_N='-n';; esac +if expr a : '\(a\)' >/dev/null 2>&1 && + test "X`expr 00001 : '.*\(...\)'`" = X001; then + as_expr=expr +else + as_expr=false +fi rm -f conf$$ conf$$.exe conf$$.file if test -d conf$$.dir; then @@ -5546,56 +6462,8 @@ fi rm -f conf$$ conf$$.exe conf$$.dir/conf$$.file conf$$.file rmdir conf$$.dir 2>/dev/null - -# as_fn_mkdir_p -# ------------- -# Create "$as_dir" as a directory, including parents if necessary. -as_fn_mkdir_p () -{ - - case $as_dir in #( - -*) as_dir=./$as_dir;; - esac - test -d "$as_dir" || eval $as_mkdir_p || { - as_dirs= - while :; do - case $as_dir in #( - *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( - *) as_qdir=$as_dir;; - esac - as_dirs="'$as_qdir' $as_dirs" - as_dir=`$as_dirname -- "$as_dir" || -$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ - X"$as_dir" : 'X\(//\)[^/]' \| \ - X"$as_dir" : 'X\(//\)$' \| \ - X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || -$as_echo X"$as_dir" | - sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ - s//\1/ - q - } - /^X\(\/\/\)[^/].*/{ - s//\1/ - q - } - /^X\(\/\/\)$/{ - s//\1/ - q - } - /^X\(\/\).*/{ - s//\1/ - q - } - s/.*/./; q'` - test -d "$as_dir" && break - done - test -z "$as_dirs" || eval "mkdir $as_dirs" - } || test -d "$as_dir" || as_fn_error $? "cannot create directory $as_dir" - - -} # as_fn_mkdir_p if mkdir -p . 2>/dev/null; then - as_mkdir_p='mkdir -p "$as_dir"' + as_mkdir_p=: else test -d ./-p && rmdir ./-p as_mkdir_p=false @@ -5614,10 +6482,10 @@ else if test -d "$1"; then test -d "$1/."; else - case $1 in #( + case $1 in -*)set "./$1";; esac; - case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in #(( + case `ls -ld'$as_ls_L_option' "$1" 2>/dev/null` in ???[sx]*):;;*)false;;esac;fi '\'' sh ' @@ -5632,19 +6500,13 @@ as_tr_sh="eval sed 'y%*+%pp%;s%[^_$as_cr_alnum]%_%g'" exec 6>&1 -## ----------------------------------- ## -## Main body of $CONFIG_STATUS script. ## -## ----------------------------------- ## -_ASEOF -test $as_write_fail = 0 && chmod +x $CONFIG_STATUS || ac_write_fail=1 -cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 -# Save the log message, to keep $0 and so on meaningful, and to +# Save the log message, to keep $[0] and so on meaningful, and to # report actual input values of CONFIG_FILES etc. instead of their # values after options handling. ac_log=" -This file was extended by gtfold $as_me 1.18, which was -generated by GNU Autoconf 2.67. Invocation command line was +This file was extended by gtfold $as_me 2.0, which was +generated by GNU Autoconf 2.63. Invocation command line was CONFIG_FILES = $CONFIG_FILES CONFIG_HEADERS = $CONFIG_HEADERS @@ -5676,15 +6538,13 @@ _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 ac_cs_usage="\ -\`$as_me' instantiates files and other configuration actions -from templates according to the current configuration. Unless the files -and actions are specified as TAGs, all are instantiated by default. +\`$as_me' instantiates files from templates according to the +current configuration. -Usage: $0 [OPTION]... [TAG]... +Usage: $0 [OPTION]... [FILE]... -h, --help print this help, then exit -V, --version print version number and configuration settings, then exit - --config print configuration, then exit -q, --quiet, --silent do not print progress messages -d, --debug don't remove temporary files @@ -5703,17 +6563,16 @@ $config_headers Configuration commands: $config_commands -Report bugs to the package provider." +Report bugs to ." _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 -ac_cs_config="`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`" ac_cs_version="\\ -gtfold config.status 1.18 -configured by $0, generated by GNU Autoconf 2.67, - with options \\"\$ac_cs_config\\" +gtfold config.status 2.0 +configured by $0, generated by GNU Autoconf 2.63, + with options \\"`$as_echo "$ac_configure_args" | sed 's/^ //; s/[\\""\`\$]/\\\\&/g'`\\" -Copyright (C) 2010 Free Software Foundation, Inc. +Copyright (C) 2008 Free Software Foundation, Inc. This config.status script is free software; the Free Software Foundation gives unlimited permission to copy, distribute and modify it." @@ -5731,16 +6590,11 @@ ac_need_defaults=: while test $# != 0 do case $1 in - --*=?*) + --*=*) ac_option=`expr "X$1" : 'X\([^=]*\)='` ac_optarg=`expr "X$1" : 'X[^=]*=\(.*\)'` ac_shift=: ;; - --*=) - ac_option=`expr "X$1" : 'X\([^=]*\)='` - ac_optarg= - ac_shift=: - ;; *) ac_option=$1 ac_optarg=$2 @@ -5754,29 +6608,27 @@ do ac_cs_recheck=: ;; --version | --versio | --versi | --vers | --ver | --ve | --v | -V ) $as_echo "$ac_cs_version"; exit ;; - --config | --confi | --conf | --con | --co | --c ) - $as_echo "$ac_cs_config"; exit ;; --debug | --debu | --deb | --de | --d | -d ) debug=: ;; --file | --fil | --fi | --f ) $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; - '') as_fn_error $? "missing file argument" ;; esac - as_fn_append CONFIG_FILES " '$ac_optarg'" + CONFIG_FILES="$CONFIG_FILES '$ac_optarg'" ac_need_defaults=false;; --header | --heade | --head | --hea ) $ac_shift case $ac_optarg in *\'*) ac_optarg=`$as_echo "$ac_optarg" | sed "s/'/'\\\\\\\\''/g"` ;; esac - as_fn_append CONFIG_HEADERS " '$ac_optarg'" + CONFIG_HEADERS="$CONFIG_HEADERS '$ac_optarg'" ac_need_defaults=false;; --he | --h) # Conflict between --help and --header - as_fn_error $? "ambiguous option: \`$1' -Try \`$0 --help' for more information.";; + { $as_echo "$as_me: error: ambiguous option: $1 +Try \`$0 --help' for more information." >&2 + { (exit 1); exit 1; }; };; --help | --hel | -h ) $as_echo "$ac_cs_usage"; exit ;; -q | -quiet | --quiet | --quie | --qui | --qu | --q \ @@ -5784,10 +6636,11 @@ Try \`$0 --help' for more information.";; ac_cs_silent=: ;; # This is an error. - -*) as_fn_error $? "unrecognized option: \`$1' -Try \`$0 --help' for more information." ;; + -*) { $as_echo "$as_me: error: unrecognized option: $1 +Try \`$0 --help' for more information." >&2 + { (exit 1); exit 1; }; } ;; - *) as_fn_append ac_config_targets " $1" + *) ac_config_targets="$ac_config_targets $1" ac_need_defaults=false ;; esac @@ -5847,8 +6700,12 @@ do "data/Turner99/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner99/Makefile" ;; "data/Turner04/Makefile") CONFIG_FILES="$CONFIG_FILES data/Turner04/Makefile" ;; "data/Andronescu/Makefile") CONFIG_FILES="$CONFIG_FILES data/Andronescu/Makefile" ;; + "data/UNAParams/Makefile") CONFIG_FILES="$CONFIG_FILES data/UNAParams/Makefile" ;; + "data/RNAParams/Makefile") CONFIG_FILES="$CONFIG_FILES data/RNAParams/Makefile" ;; - *) as_fn_error $? "invalid argument: \`$ac_config_target'" "$LINENO" 5 ;; + *) { { $as_echo "$as_me:$LINENO: error: invalid argument: $ac_config_target" >&5 +$as_echo "$as_me: error: invalid argument: $ac_config_target" >&2;} + { (exit 1); exit 1; }; };; esac done @@ -5875,7 +6732,7 @@ $debug || trap 'exit_status=$? { test -z "$tmp" || test ! -d "$tmp" || rm -fr "$tmp"; } && exit $exit_status ' 0 - trap 'as_fn_exit 1' 1 2 13 15 + trap '{ (exit 1); exit 1; }' 1 2 13 15 } # Create a (secure) tmp directory for tmp files. @@ -5886,7 +6743,11 @@ $debug || { tmp=./conf$$-$RANDOM (umask 077 && mkdir "$tmp") -} || as_fn_error $? "cannot create a temporary directory in ." "$LINENO" 5 +} || +{ + $as_echo "$as_me: cannot create a temporary directory in ." >&2 + { (exit 1); exit 1; } +} # Set up the scripts for CONFIG_FILES section. # No need to generate them if there are no CONFIG_FILES. @@ -5894,13 +6755,7 @@ $debug || if test -n "$CONFIG_FILES"; then -ac_cr=`echo X | tr X '\015'` -# On cygwin, bash can eat \r inside `` if the user requested igncr. -# But we know of no other shell where ac_cr would be empty at this -# point, so we can use a bashism as a fallback. -if test "x$ac_cr" = x; then - eval ac_cr=\$\'\\r\' -fi +ac_cr=' ' ac_cs_awk_cr=`$AWK 'BEGIN { print "a\rb" }' /dev/null` if test "$ac_cs_awk_cr" = "a${ac_cr}b"; then ac_cs_awk_cr='\\r' @@ -5917,18 +6772,24 @@ _ACEOF echo "$ac_subst_vars" | sed 's/.*/&!$&$ac_delim/' && echo "_ACEOF" } >conf$$subs.sh || - as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 -ac_delim_num=`echo "$ac_subst_vars" | grep -c '^'` + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } +ac_delim_num=`echo "$ac_subst_vars" | grep -c '$'` ac_delim='%!_!# ' for ac_last_try in false false false false false :; do . ./conf$$subs.sh || - as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } ac_delim_n=`sed -n "s/.*$ac_delim\$/X/p" conf$$subs.awk | grep -c X` if test $ac_delim_n = $ac_delim_num; then break elif $ac_last_try; then - as_fn_error $? "could not make $CONFIG_STATUS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi @@ -5950,7 +6811,7 @@ s/'"$ac_delim"'$// t delim :nl h -s/\(.\{148\}\)..*/\1/ +s/\(.\{148\}\).*/\1/ t more1 s/["\\]/\\&/g; s/^/"/; s/$/\\n"\\/ p @@ -5964,7 +6825,7 @@ s/.\{148\}// t nl :delim h -s/\(.\{148\}\)..*/\1/ +s/\(.\{148\}\).*/\1/ t more2 s/["\\]/\\&/g; s/^/"/; s/$/"/ p @@ -6017,28 +6878,22 @@ if sed "s/$ac_cr//" < /dev/null > /dev/null 2>&1; then else cat fi < "$tmp/subs1.awk" > "$tmp/subs.awk" \ - || as_fn_error $? "could not setup config files machinery" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not setup config files machinery" >&5 +$as_echo "$as_me: error: could not setup config files machinery" >&2;} + { (exit 1); exit 1; }; } _ACEOF -# VPATH may cause trouble with some makes, so we remove sole $(srcdir), -# ${srcdir} and @srcdir@ entries from VPATH if srcdir is ".", strip leading and +# VPATH may cause trouble with some makes, so we remove $(srcdir), +# ${srcdir} and @srcdir@ from VPATH if srcdir is ".", strip leading and # trailing colons and then remove the whole line if VPATH becomes empty # (actually we leave an empty line to preserve line numbers). if test "x$srcdir" = x.; then - ac_vpsub='/^[ ]*VPATH[ ]*=[ ]*/{ -h -s/// -s/^/:/ -s/[ ]*$/:/ -s/:\$(srcdir):/:/g -s/:\${srcdir}:/:/g -s/:@srcdir@:/:/g -s/^:*// + ac_vpsub='/^[ ]*VPATH[ ]*=/{ +s/:*\$(srcdir):*/:/ +s/:*\${srcdir}:*/:/ +s/:*@srcdir@:*/:/ +s/^\([^=]*=[ ]*\):*/\1/ s/:*$// -x -s/\(=[ ]*\).*/\1/ -G -s/\n// s/^[^=]*=[ ]*$// }' fi @@ -6066,7 +6921,9 @@ for ac_last_try in false false :; do if test -z "$ac_t"; then break elif $ac_last_try; then - as_fn_error $? "could not make $CONFIG_HEADERS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not make $CONFIG_HEADERS" >&5 +$as_echo "$as_me: error: could not make $CONFIG_HEADERS" >&2;} + { (exit 1); exit 1; }; } else ac_delim="$ac_delim!$ac_delim _$ac_delim!! " fi @@ -6151,7 +7008,9 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 _ACAWK _ACEOF cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 - as_fn_error $? "could not setup config headers machinery" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: could not setup config headers machinery" >&5 +$as_echo "$as_me: error: could not setup config headers machinery" >&2;} + { (exit 1); exit 1; }; } fi # test -n "$CONFIG_HEADERS" @@ -6164,7 +7023,9 @@ do esac case $ac_mode$ac_tag in :[FHL]*:*);; - :L* | :C*:*) as_fn_error $? "invalid tag \`$ac_tag'" "$LINENO" 5 ;; + :L* | :C*:*) { { $as_echo "$as_me:$LINENO: error: invalid tag $ac_tag" >&5 +$as_echo "$as_me: error: invalid tag $ac_tag" >&2;} + { (exit 1); exit 1; }; };; :[FH]-) ac_tag=-:-;; :[FH]*) ac_tag=$ac_tag:$ac_tag.in;; esac @@ -6192,10 +7053,12 @@ do [\\/$]*) false;; *) test -f "$srcdir/$ac_f" && ac_f="$srcdir/$ac_f";; esac || - as_fn_error 1 "cannot find input file: \`$ac_f'" "$LINENO" 5 ;; + { { $as_echo "$as_me:$LINENO: error: cannot find input file: $ac_f" >&5 +$as_echo "$as_me: error: cannot find input file: $ac_f" >&2;} + { (exit 1); exit 1; }; };; esac case $ac_f in *\'*) ac_f=`$as_echo "$ac_f" | sed "s/'/'\\\\\\\\''/g"`;; esac - as_fn_append ac_file_inputs " '$ac_f'" + ac_file_inputs="$ac_file_inputs '$ac_f'" done # Let's still pretend it is `configure' which instantiates (i.e., don't @@ -6206,7 +7069,7 @@ do `' by configure.' if test x"$ac_file" != x-; then configure_input="$ac_file. $configure_input" - { $as_echo "$as_me:${as_lineno-$LINENO}: creating $ac_file" >&5 + { $as_echo "$as_me:$LINENO: creating $ac_file" >&5 $as_echo "$as_me: creating $ac_file" >&6;} fi # Neutralize special characters interpreted by sed in replacement strings. @@ -6219,7 +7082,9 @@ $as_echo "$as_me: creating $ac_file" >&6;} case $ac_tag in *:-:* | *:-) cat >"$tmp/stdin" \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 ;; + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } ;; esac ;; esac @@ -6247,7 +7112,47 @@ $as_echo X"$ac_file" | q } s/.*/./; q'` - as_dir="$ac_dir"; as_fn_mkdir_p + { as_dir="$ac_dir" + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5 +$as_echo "$as_me: error: cannot create directory $as_dir" >&2;} + { (exit 1); exit 1; }; }; } ac_builddir=. case "$ac_dir" in @@ -6304,6 +7209,7 @@ cat >>$CONFIG_STATUS <<\_ACEOF || ac_write_fail=1 # If the template does not know about datarootdir, expand it. # FIXME: This hack should be removed a few years after 2.60. ac_datarootdir_hack=; ac_datarootdir_seen= + ac_sed_dataroot=' /datarootdir/ { p @@ -6313,11 +7219,12 @@ ac_sed_dataroot=' /@docdir@/p /@infodir@/p /@localedir@/p -/@mandir@/p' +/@mandir@/p +' case `eval "sed -n \"\$ac_sed_dataroot\" $ac_file_inputs"` in *datarootdir*) ac_datarootdir_seen=yes;; *@datadir@*|*@docdir@*|*@infodir@*|*@localedir@*|*@mandir@*) - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 + { $as_echo "$as_me:$LINENO: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&5 $as_echo "$as_me: WARNING: $ac_file_inputs seems to ignore the --datarootdir setting" >&2;} _ACEOF cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 @@ -6327,7 +7234,7 @@ cat >>$CONFIG_STATUS <<_ACEOF || ac_write_fail=1 s&@infodir@&$infodir&g s&@localedir@&$localedir&g s&@mandir@&$mandir&g - s&\\\${datarootdir}&$datarootdir&g' ;; + s&\\\${datarootdir}&$datarootdir&g' ;; esac _ACEOF @@ -6356,22 +7263,26 @@ s&@MKDIR_P@&$ac_MKDIR_P&;t t $ac_datarootdir_hack " eval sed \"\$ac_sed_extra\" "$ac_file_inputs" | $AWK -f "$tmp/subs.awk" >$tmp/out \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } test -z "$ac_datarootdir_hack$ac_datarootdir_seen" && { ac_out=`sed -n '/\${datarootdir}/p' "$tmp/out"`; test -n "$ac_out"; } && { ac_out=`sed -n '/^[ ]*datarootdir[ ]*:*=/p' "$tmp/out"`; test -z "$ac_out"; } && - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: $ac_file contains a reference to the variable \`datarootdir' -which seems to be undefined. Please make sure it is defined" >&5 + { $as_echo "$as_me:$LINENO: WARNING: $ac_file contains a reference to the variable \`datarootdir' +which seems to be undefined. Please make sure it is defined." >&5 $as_echo "$as_me: WARNING: $ac_file contains a reference to the variable \`datarootdir' -which seems to be undefined. Please make sure it is defined" >&2;} +which seems to be undefined. Please make sure it is defined." >&2;} rm -f "$tmp/stdin" case $ac_file in -) cat "$tmp/out" && rm -f "$tmp/out";; *) rm -f "$ac_file" && mv "$tmp/out" "$ac_file";; esac \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } ;; :H) # @@ -6382,19 +7293,25 @@ which seems to be undefined. Please make sure it is defined" >&2;} $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" } >"$tmp/config.h" \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } if diff "$ac_file" "$tmp/config.h" >/dev/null 2>&1; then - { $as_echo "$as_me:${as_lineno-$LINENO}: $ac_file is unchanged" >&5 + { $as_echo "$as_me:$LINENO: $ac_file is unchanged" >&5 $as_echo "$as_me: $ac_file is unchanged" >&6;} else rm -f "$ac_file" mv "$tmp/config.h" "$ac_file" \ - || as_fn_error $? "could not create $ac_file" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create $ac_file" >&5 +$as_echo "$as_me: error: could not create $ac_file" >&2;} + { (exit 1); exit 1; }; } fi else $as_echo "/* $configure_input */" \ && eval '$AWK -f "$tmp/defines.awk"' "$ac_file_inputs" \ - || as_fn_error $? "could not create -" "$LINENO" 5 + || { { $as_echo "$as_me:$LINENO: error: could not create -" >&5 +$as_echo "$as_me: error: could not create -" >&2;} + { (exit 1); exit 1; }; } fi # Compute "$ac_file"'s index in $config_headers. _am_arg="$ac_file" @@ -6432,7 +7349,7 @@ $as_echo X"$_am_arg" | s/.*/./; q'`/stamp-h$_am_stamp_count ;; - :C) { $as_echo "$as_me:${as_lineno-$LINENO}: executing $ac_file commands" >&5 + :C) { $as_echo "$as_me:$LINENO: executing $ac_file commands" >&5 $as_echo "$as_me: executing $ac_file commands" >&6;} ;; esac @@ -6527,7 +7444,47 @@ $as_echo X"$file" | q } s/.*/./; q'` - as_dir=$dirpart/$fdir; as_fn_mkdir_p + { as_dir=$dirpart/$fdir + case $as_dir in #( + -*) as_dir=./$as_dir;; + esac + test -d "$as_dir" || { $as_mkdir_p && mkdir -p "$as_dir"; } || { + as_dirs= + while :; do + case $as_dir in #( + *\'*) as_qdir=`$as_echo "$as_dir" | sed "s/'/'\\\\\\\\''/g"`;; #'( + *) as_qdir=$as_dir;; + esac + as_dirs="'$as_qdir' $as_dirs" + as_dir=`$as_dirname -- "$as_dir" || +$as_expr X"$as_dir" : 'X\(.*[^/]\)//*[^/][^/]*/*$' \| \ + X"$as_dir" : 'X\(//\)[^/]' \| \ + X"$as_dir" : 'X\(//\)$' \| \ + X"$as_dir" : 'X\(/\)' \| . 2>/dev/null || +$as_echo X"$as_dir" | + sed '/^X\(.*[^/]\)\/\/*[^/][^/]*\/*$/{ + s//\1/ + q + } + /^X\(\/\/\)[^/].*/{ + s//\1/ + q + } + /^X\(\/\/\)$/{ + s//\1/ + q + } + /^X\(\/\).*/{ + s//\1/ + q + } + s/.*/./; q'` + test -d "$as_dir" && break + done + test -z "$as_dirs" || eval "mkdir $as_dirs" + } || test -d "$as_dir" || { { $as_echo "$as_me:$LINENO: error: cannot create directory $as_dir" >&5 +$as_echo "$as_me: error: cannot create directory $as_dir" >&2;} + { (exit 1); exit 1; }; }; } # echo "creating $dirpart/$file" echo '# dummy' > "$dirpart/$file" done @@ -6539,12 +7496,15 @@ $as_echo X"$file" | done # for ac_tag -as_fn_exit 0 +{ (exit 0); exit 0; } _ACEOF +chmod +x $CONFIG_STATUS ac_clean_files=$ac_clean_files_save test $ac_write_fail = 0 || - as_fn_error $? "write failure creating $CONFIG_STATUS" "$LINENO" 5 + { { $as_echo "$as_me:$LINENO: error: write failure creating $CONFIG_STATUS" >&5 +$as_echo "$as_me: error: write failure creating $CONFIG_STATUS" >&2;} + { (exit 1); exit 1; }; } # configure is writing to config.log, and then calls config.status. @@ -6565,10 +7525,10 @@ if test "$no_create" != yes; then exec 5>>config.log # Use ||, not &&, to avoid exiting from the if with $? = 1, which # would make configure fail if this is the last instruction. - $ac_cs_success || as_fn_exit 1 + $ac_cs_success || { (exit 1); exit 1; } fi if test -n "$ac_unrecognized_opts" && test "$enable_option_checking" != no; then - { $as_echo "$as_me:${as_lineno-$LINENO}: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 + { $as_echo "$as_me:$LINENO: WARNING: unrecognized options: $ac_unrecognized_opts" >&5 $as_echo "$as_me: WARNING: unrecognized options: $ac_unrecognized_opts" >&2;} fi diff --git a/gtfold-mfe/configure.in b/gtfold-mfe/configure.in index b5b456b..0643019 100644 --- a/gtfold-mfe/configure.in +++ b/gtfold-mfe/configure.in @@ -1,22 +1,22 @@ dnl Process this file with autoconf to produce a configure script. -dnl AC_PREREQ(1.8) +dnl AC_PREREQ([2.67]) dnl AC 2.62 needed for OpenMP -AC_PREREQ(2.62) +AC_PREREQ([2.63]) dnl AC_INIT (package, version, [bug-report-email], [tarname]) -AC_INIT([gtfold],[1.18]) +AC_INIT([gtfold],[2.0]) dnl check for this file's existence to make sure that the directory dnl specified by --srcdir is the right one AC_CONFIG_SRCDIR([README]) dnl Specify a header configuration file -AM_CONFIG_HEADER(gtfold_config.h) +AC_CONFIG_HEADERS([gtfold_config.h]) dnl Compute the canonical host-system type variable, host, and its dnl three individual parts host_cpu, host_vendor, and host_os. -AC_CANONICAL_SYSTEM +AC_CANONICAL_TARGET dnl Initialize Automake AM_INIT_AUTOMAKE @@ -62,7 +62,7 @@ dnl Check for libraries AC_CHECK_LIB(m, log2, AC_DEFINE([HAVE_LOG2],[],[log2 function is present])) dnl Check for header files -AC_STDC_HEADERS +AC_HEADER_STDC #AC_CHECK_HEADERS(sys/resource.h) #AC_CHECK_HEADERS(getopt.h) AC_CHECK_HEADERS([stdlib.h string.h sys/time.h]) @@ -99,27 +99,23 @@ fi dnl This is an example how to check for compiler characteristics that dnl are not a part of the standard Autoconf tests: -If Sun cc is present, define appropriate compiler flags +#If Sun cc is present, define appropriate compiler flags AC_MSG_CHECKING(for Sun C compiler) -AC_TRY_COMPILE([], [#ifndef __SUNPRO_C +AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __SUNPRO_C #include "error: this is not a Sun C compiler." #endif - ], - [AC_MSG_RESULT(yes) - gtfold_cv_check_sunpro_cc=yes], - [AC_MSG_RESULT(no) + ]])],[AC_MSG_RESULT(yes) + gtfold_cv_check_sunpro_cc=yes],[AC_MSG_RESULT(no) gtfold_cv_check_sunpro_cc=no]) if test "$gtfold_cv_check_sunpro_cc" == "yes"; then AC_MSG_CHECKING(for Sun C compiler architecture target) - AC_TRY_COMPILE([], [#ifndef __sparc + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparc #include "error: this is not a Sun Sparc processor." #endif - ], - [AC_MSG_RESULT(yes) - gtfold_cv_check_sun_sparc=yes], - [AC_MSG_RESULT(no) + ]])],[AC_MSG_RESULT(yes) + gtfold_cv_check_sun_sparc=yes],[AC_MSG_RESULT(no) gtfold_cv_check_sun_sparc=no]) fi @@ -128,13 +124,11 @@ then if test "$gtfold_cv_check_sun_sparc" == "yes"; then AC_MSG_CHECKING(for Sun sparc v9 architecture) - AC_TRY_COMPILE([], [#ifndef __sparcv9 + AC_COMPILE_IFELSE([AC_LANG_PROGRAM([[]], [[#ifndef __sparcv9 #include "error: this is not a Sun Sparc V9 processor." #endif - ], - [AC_MSG_RESULT(yes) - gtfold_cv_check_sun_sparcv9=yes], - [AC_MSG_RESULT(no) + ]])],[AC_MSG_RESULT(yes) + gtfold_cv_check_sun_sparcv9=yes],[AC_MSG_RESULT(no) gtfold_cv_check_sun_sparcv9=no]) fi fi @@ -184,7 +178,7 @@ AM_CONDITIONAL(GTFOLD_DEBUG, test x$debug = xtrue) dnl Create makefiles and other configuration files AC_CONFIG_FILES([Makefile src/Makefile data/Makefile include/Makefile]) -AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile]) +AC_CONFIG_FILES([data/Turner99/Makefile data/Turner04/Makefile data/Andronescu/Makefile data/UNAParams/Makefile data/RNAParams/Makefile]) dnl Generate `config.status' and launch it AC_OUTPUT diff --git a/gtfold-mfe/createsymlinks.sh b/gtfold-mfe/createsymlinks.sh new file mode 100644 index 0000000..1427a56 --- /dev/null +++ b/gtfold-mfe/createsymlinks.sh @@ -0,0 +1,14 @@ +#!/bin/sh +if [ $# != 1 ] +then +echo "Usage: sh createsymlinks.sh " +exit -1 +fi + +BINDIR=$1 +echo 'creating symlinks under' $BINDIR +cd $BINDIR +ln -sf gtfold gtmfe +ln -sf gtfold gtsubopt +ln -sf gtfold gtboltzmann + diff --git a/gtfold-mfe/data/Makefile.am b/gtfold-mfe/data/Makefile.am index d9d1d43..001e73e 100644 --- a/gtfold-mfe/data/Makefile.am +++ b/gtfold-mfe/data/Makefile.am @@ -1,2 +1,2 @@ -SUBDIRS = Turner04 Turner99 Andronescu +SUBDIRS = UNAParams RNAParams Turner04 Turner99 Andronescu diff --git a/gtfold-mfe/data/Makefile.in b/gtfold-mfe/data/Makefile.in index 20b49f3..a245c3c 100644 --- a/gtfold-mfe/data/Makefile.in +++ b/gtfold-mfe/data/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -128,7 +128,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -190,7 +189,7 @@ target_vendor = @target_vendor@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -SUBDIRS = Turner04 Turner99 Andronescu +SUBDIRS = UNAParams RNAParams Turner04 Turner99 Andronescu all: all-recursive .SUFFIXES: @@ -232,7 +231,7 @@ $(am__aclocal_m4_deps): # (which will cause the Makefiles to be regenerated when you run `make'); # (2) otherwise, pass the desired values on the `make' command line. $(RECURSIVE_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ @@ -257,7 +256,7 @@ $(RECURSIVE_TARGETS): fi; test -z "$$fail" $(RECURSIVE_CLEAN_TARGETS): - @fail= failcom='exit 1'; \ + @failcom='exit 1'; \ for f in x $$MAKEFLAGS; do \ case $$f in \ *=* | --[!k]*);; \ diff --git a/gtfold-mfe/data/RNAParams/Makefile.am b/gtfold-mfe/data/RNAParams/Makefile.am new file mode 100644 index 0000000..8655bda --- /dev/null +++ b/gtfold-mfe/data/RNAParams/Makefile.am @@ -0,0 +1,23 @@ +## Process this file with automake to produce Makefile.in + +gtfold_datadir = $(datadir)/@PACKAGE@/RNAParams + +gtfold_data_DATA = \ + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstacke.DAT\ + tstackm.DAT + + +EXTRA_DIST = $(gtfold_data_DATA) + 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2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.10 2.20 2.20 2.00 2.30 2.20 2.00 2.20 2.20 2.00 2.40 1.00 2.00 2.20 2.00 1.40 + 1.70 1.50 0.50 2.00 1.60 2.40 2.00 2.40 0.50 2.00 1.00 1.10 2.00 2.40 2.10 2.40 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 2.10 1.90 0.90 2.00 2.00 2.40 2.00 2.40 0.90 2.00 1.40 0.70 2.00 2.40 1.70 2.00 + 2.20 1.00 1.80 2.00 1.10 1.90 2.00 1.90 1.80 2.00 1.50 -1.20 2.00 1.90 -0.20 1.90 + 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 + 3.40 2.50 2.50 2.00 2.60 2.50 2.00 2.50 2.50 2.00 2.70 1.30 2.00 2.50 2.30 1.70 + 1.00 -0.30 0.50 2.00 -0.20 0.70 2.00 0.70 0.50 2.00 0.30 -2.50 2.00 0.70 -1.50 0.70 + 2.90 1.70 2.50 2.00 1.80 1.60 2.00 1.60 2.50 2.00 2.20 1.30 2.00 1.60 2.30 0.80 diff --git a/gtfold-mfe/data/RNAParams/loop.DAT b/gtfold-mfe/data/RNAParams/loop.DAT new file mode 100644 index 0000000..98c1285 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/loop.DAT @@ -0,0 +1,30 @@ +1 inf 3.80 inf +2 4.10 2.80 inf +3 5.10 3.20 5.70 +4 1.70 3.60 5.60 +5 1.80 4.00 5.60 +6 2.00 4.40 5.40 +7 2.20 4.59 5.90 +8 2.30 4.70 5.60 +9 2.40 4.80 6.40 +10 2.50 4.90 6.50 +11 2.60 5.00 6.60 +12 2.70 5.10 6.70 +13 2.78 5.19 6.78 +14 2.86 5.27 6.86 +15 2.94 5.34 6.94 +16 3.01 5.41 7.01 +17 3.07 5.48 7.07 +18 3.13 5.54 7.13 +19 3.19 5.60 7.19 +20 3.25 5.65 7.25 +21 3.30 5.71 7.30 +22 3.35 5.76 7.35 +23 3.40 5.80 7.40 +24 3.45 5.85 7.44 +25 3.49 5.89 7.49 +26 3.53 5.94 7.53 +27 3.57 5.98 7.57 +28 3.61 6.02 7.61 +29 3.65 6.05 7.65 +30 3.69 6.09 7.69 diff --git a/gtfold-mfe/data/RNAParams/miscloop.DAT b/gtfold-mfe/data/RNAParams/miscloop.DAT new file mode 100644 index 0000000..69847f3 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/miscloop.DAT @@ -0,0 +1,12 @@ +1.079 +3.00 +.50 .50 .50 .50 +3.40 .00 .40 +10.10 -0.30 -0.30 +0.50 +0.0 +0.0 +0.0 +0.0 +4.10 +0 diff --git a/gtfold-mfe/data/RNAParams/sint2.DAT b/gtfold-mfe/data/RNAParams/sint2.DAT new file mode 100644 index 0000000..96eabfd --- /dev/null +++ b/gtfold-mfe/data/RNAParams/sint2.DAT @@ -0,0 +1,24 @@ +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.50 1.10 1.10 1.10 1.00 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.20 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.10 1.10 1.10 1.10 0.40 -0.40 0.40 0.40 1.10 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 +1.10 1.10 1.10 1.10 0.30 0.50 0.40 0.50 0.40 0.40 0.40 0.40 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 +1.10 1.10 -1.00 1.10 -0.10 0.40 -1.70 0.40 0.40 0.40 -1.40 0.40 1.10 1.10 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1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.80 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.50 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 +1.70 1.70 -0.40 1.70 1.10 1.10 -1.00 1.10 1.10 1.10 -1.00 1.10 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 1.70 1.70 -0.40 1.70 +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 diff --git a/gtfold-mfe/data/RNAParams/sint4.DAT b/gtfold-mfe/data/RNAParams/sint4.DAT new file mode 100644 index 0000000..c878345 --- /dev/null +++ b/gtfold-mfe/data/RNAParams/sint4.DAT @@ -0,0 +1,576 @@ +2.80 2.30 1.70 2.00 2.80 3.40 2.00 3.40 1.70 2.00 2.10 1.00 2.00 3.10 2.20 2.90 +2.60 2.20 1.60 2.00 2.60 2.60 2.00 2.60 1.60 2.00 2.00 -0.20 2.00 2.30 1.10 1.80 +1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +2.50 2.10 1.50 2.00 2.50 2.50 2.00 2.50 1.50 2.00 1.90 -0.30 2.00 2.20 1.00 1.70 +3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 +1.50 1.10 0.50 2.00 1.50 2.50 2.00 2.50 0.50 2.00 0.90 0.50 2.00 2.20 1.80 2.50 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +2.10 1.60 1.00 2.00 2.10 2.70 2.00 2.70 1.00 2.00 1.40 0.30 2.00 2.40 1.50 2.20 +2.30 0.90 2.10 2.00 1.30 2.30 2.00 2.30 2.10 2.00 1.70 -1.50 2.00 2.00 -0.20 2.30 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +3.10 2.00 2.40 2.00 2.50 2.50 2.00 2.50 2.40 2.00 2.40 0.70 2.00 2.20 1.90 1.60 +1.30 -0.10 1.10 2.00 0.30 1.30 2.00 1.30 1.10 2.00 0.70 -2.50 2.00 1.00 -1.20 1.30 +2.70 1.20 2.40 2.00 1.70 1.70 2.00 1.70 2.40 2.00 2.00 0.70 2.00 1.40 1.90 0.80 +2.10 1.90 0.10 2.00 1.80 2.50 2.00 1.50 0.70 2.00 1.80 0.00 2.00 2.50 0.40 2.10 +2.00 1.70 0.00 2.00 1.70 1.70 2.00 0.70 0.60 2.00 1.60 -1.20 2.00 1.80 -0.80 1.00 +0.90 0.60 -1.10 2.00 0.60 1.60 2.00 0.70 -0.50 2.00 0.50 -0.50 2.00 1.70 -0.10 1.70 +2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 2.00 +1.90 1.60 -0.10 2.00 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html html-am info info-am \ + install install-am install-data install-data-am install-dvi \ + install-dvi-am install-exec install-exec-am \ + install-gtfold_dataDATA install-html install-html-am \ + install-info install-info-am install-man install-pdf \ + install-pdf-am install-ps install-ps-am install-strip \ + installcheck installcheck-am installdirs maintainer-clean \ + maintainer-clean-generic mostlyclean mostlyclean-generic pdf \ + pdf-am ps ps-am uninstall uninstall-am \ + uninstall-gtfold_dataDATA + + +# Tell versions [3.59,3.63) of GNU make to not export all variables. +# Otherwise a system limit (for SysV at least) may be exceeded. +.NOEXPORT: diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am b/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am new file mode 100644 index 0000000..302a135 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/Makefile.am @@ -0,0 +1,27 @@ +## Process this file with automake to produce Makefile.in + +gtfold_datadir = $(datadir)/@PACKAGE@/Turner04 + +gtfold_data_DATA = \ + stack.dat\ + miscloop.dat\ + dangle.dat\ + loop.dat\ + coaxial.dat\ + coaxstack.dat\ + hexaloop.dat\ + int11.dat\ + int21.dat\ + int22.dat\ + tloop.dat\ + triloop.dat\ + tstack.dat\ + tstackcoax.dat\ + tstackh.dat\ + tstacki.dat\ + tstackm.dat + +EXTRA_DIST = $(gtfold_data_DATA) + +CLEANFILES = *~ + diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat new file mode 100644 index 0000000..1fb3051 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxial.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +ERRORS IN STACKING ENERGIES : + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat new file mode 100644 index 0000000..cef509d --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/coaxstack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +ERRORS IN STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat new file mode 100644 index 0000000..7c9161b --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/dangle.dat @@ -0,0 +1,72 @@ + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + A C G U + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + A A A A + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + C C C C + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + G G G G + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + X X X X +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + U U U U + AX CX GX UX + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat new file mode 100644 index 0000000..66eb771 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/hexaloop.dat @@ -0,0 +1,6 @@ + Seq Energy + ------------- + ACAGUGCU 0 + ACAGUGAU 0 + ACAGUUCU 0 + ACAGUACU 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat new file mode 100644 index 0000000..67aa76a --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int11.dat @@ -0,0 +1,101 @@ +Data table for symetric interior loops of size 2 +Free energies at 37 degrees for RNA +Data Arrangement: + Y + ------------------ +(X) A C G U + ------------------ + 5' --> 3' + X + A A + U U + Y + 3' <-- 5' +(A) . . . . +(C) . . . . +(G) . . . . +(U) . . . . + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + C A C C C G C U C G C U + G U G G G C G A G U G G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 -0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + C U C G C C C A C U C G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + A U A G A C A A A U A G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + G A G C G G G U G G G U + U U U G U C U A U U U G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + U A U C U G U U U G U U + G U G G G C G A G U G G + Y Y Y Y Y Y + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 + 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 0.00 0.00 -0.00 0.00 + 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat new file mode 100644 index 0000000..9966877 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/int21.dat @@ -0,0 +1,353 @@ +Data tables for asymmetric interior loops of size 3 +Free energies at 37 degrees for RNA +Data arrangement: + Y + ------------------ +(X) A C G U + ------------------ + 5' --> 3' + X + A A + U U + YA + 3' <-- 5' +(A) . . . . +(C) . . . . +(G) . . . . +(U) . . . . + Y Y Y Y Y Y + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U A C G U A C G U + ------------------ ------------------ ------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + X X X X X X + A A A C A G A U A G A U + U U U G U C U A U U U G + YA YA YA YA YA YA + 3' <-- 5' 3' <-- 5' 3' <-- 5' 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(INTERPOLATE WHERE NEEDED) +hp3 ave calc no tmm;hp4 ave calc with tmm; ave all bulges +SIZE INTERNAL BULGE HAIRPIN +------------------------------------------------------- +1 0 0.08 0 +2 0 1.3 0 +3 0 1.9 0.2 +4 0.1 0 0.1 +5 0.1 0 0.2 +6 0.1 0 0.1 +7 0.1 0 0.2 +8 0 0 0.2 +9 0 0 0.2 +10 0 0 0 +11 0 0 0 +12 0 0 0 +13 0 0 0 +14 0 0 0 +15 0 0 0 +16 0 0 0 +17 0 0 0 +18 0 0 0 +19 0 0 0 +20 0 0 0 +21 0 0 0 +22 0 0 0 +23 0 0 0 +24 0 0 0 +25 0 0 0 +26 0 0 0 +27 0 0 0 +28 0 0 0 +29 0 0 0 +30 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat new file mode 100644 index 0000000..c9b76e9 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/miscloop.dat @@ -0,0 +1,48 @@ +Miscellaneous free energy rules +------------------------------- +Extrapolation for large loops based on polymer theory +internal, bulge or hairpin loops > 30: dS(T)=dS(30)+param*ln(n/30) +--> +1.079 +asymmetric internal loops: the ninio equation +the maximum correction +--> +3.0 +the f(m) array (see Ninio for details) +--> + .6 .6 .6 .6 +multibranched loops + offset, per nuc penalty, helix penalty +--> + 9.3 -.0 -.9 +efn2 multibranched loops + offset, per nuc penalty, helix penalty +--> + 9.3 0.0 -0.9 +miscloop asym +--> +0.9 +multiloop strain +--> +0.44 +terminal AU penalty +--> + 0.5 +bonus for GGG hairpin +--> +-2.2 +c hairpin slope +--> +0.3 +c hairpin intercept +--> +0.24 +c hairpin of 3 +--> +1.5 +Intermolecular initiation free energy +--> +4.1 +Bonus for Single C bulges adjacent to C +--> +0.3 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat new file mode 100644 index 0000000..81fa1e6 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/stack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) 0 0 0 0 + (C) 0 0 0 0 + (G) 0 0 0 0 + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.03 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0.06 0 + 0 0 0 0 0 0 0 0 0 0 0 0 0 0.07 0 0.32 + 0 0 0 0 0 0 0 0 0 0 0 0 0.08 0 0.24 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0 0 0 0 0.07 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0 0.07 0 0 0 0 0 + 0 0 0 0 0 0 0 0 0 0.09 0 0.27 0 0 0 0 + 0 0 0 0 0 0 0 0 0.06 0 0.24 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0 0 0 0 0.06 0 0 0 0 0 0 0 0.28 + 0 0 0 0 0 0 0.08 0 0 0 0 0 0 0 0.25 0 + 0 0 0 0 0 0.07 0 0.27 0 0 0 0 0 0.25 0 0.96 + 0 0 0 0 0.06 0 0.25 0 0 0 0 0 0.24 0 0.56 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' + 0 0 0 0.09 0 0 0 0 0 0 0 0.30 0 0 0 0 + 0 0 0.06 0 0 0 0 0 0 0 0.27 0 0 0 0 0 + 0 0.07 0 0.30 0 0 0 0 0 0.24 0 0.48 0 0 0 0 +0.03 0 0.28 0 0 0 0 0 0.32 0 0.96 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat new file mode 100644 index 0000000..3a63c62 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tloop.dat @@ -0,0 +1,17 @@ + Seq Energy + ------------- +CUACGG 0 +CUCCGG 0 +CUUCGG 0 +CCAAGG 0 +CCCAGG 0 +CCGAGG 0 +CCUAGG 0 +CCACGG 0 +CCGCGG 0 +CCUCGG 0 +CUAAGG 0 +CUCAGG 0 +CUUAGG 0 +CUGCGG 0 +CAACGG 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat new file mode 100644 index 0000000..e66a4b6 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/triloop.dat @@ -0,0 +1,4 @@ + Seq Energy + ------------- +CAACG 0 +GUUAC 0 \ No newline at end of file diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstack.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 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Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackh.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstacki.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat new file mode 100644 index 0000000..6ab5d45 --- /dev/null +++ b/gtfold-mfe/data/Turner04-errors/Turner04-errors/tstackm.dat @@ -0,0 +1,63 @@ +Data Arangement: + Y + ------------------ + (X) A C G U + ------------------ + 5' ==> 3' + AX + AY + 3' <== 5' + (A) . . . . + (C) . . . . + (G) . . . . + (U) -0.7 -0.1 -0.7 -0.1 +-------------------------------- +STACKING ENERGIES : TERMINAL MISMATCHES AND BASE-PAIRS. + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + AX AX AX AX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + CX CX CX CX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + GX GX GX GX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 + Y Y Y Y +------------------ ------------------ ------------------ ------------------ + A C G U A C G U A C G U A C G U +------------------ ------------------ ------------------ ------------------ + 5' --> 3' 5' --> 3' 5' --> 3' 5' --> 3' + UX UX UX UX + AY CY GY UY + 3' <-- 5' 3' <-- 5' 3' <-- 5' 3' <-- 5' +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 diff --git a/gtfold-mfe/data/Turner99/Makefile.am b/gtfold-mfe/data/Turner99/Makefile.am index 4cf8fa7..4390f87 100644 --- a/gtfold-mfe/data/Turner99/Makefile.am +++ b/gtfold-mfe/data/Turner99/Makefile.am @@ -3,25 +3,19 @@ gtfold_datadir = $(datadir)/@PACKAGE@/Turner99 gtfold_data_DATA = \ - stack.dat\ - miscloop.dat\ - dangle.dat\ - loop.dat\ - asint1x2.dat\ - coaxial.dat\ - coaxstack.dat\ - int11.dat\ - int21.dat\ - int22.dat\ - sint2.dat\ - sint4.dat\ - tloop.dat\ - triloop.dat\ - tstack.dat\ - tstackcoax.dat\ - tstackh.dat\ - tstacki.dat\ - tstackm.dat + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstacke.DAT\ + tstackm.DAT + EXTRA_DIST = $(gtfold_data_DATA) diff --git a/gtfold-mfe/data/Turner99/Makefile.in b/gtfold-mfe/data/Turner99/Makefile.in index d9a1eb3..d21f2af 100644 --- a/gtfold-mfe/data/Turner99/Makefile.in +++ b/gtfold-mfe/data/Turner99/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -112,7 +112,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -176,25 +175,18 @@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ gtfold_datadir = $(datadir)/@PACKAGE@/Turner99 gtfold_data_DATA = \ - stack.dat\ - miscloop.dat\ - dangle.dat\ - loop.dat\ - asint1x2.dat\ - coaxial.dat\ - coaxstack.dat\ - int11.dat\ - int21.dat\ - int22.dat\ - sint2.dat\ - sint4.dat\ - tloop.dat\ - triloop.dat\ - tstack.dat\ - tstackcoax.dat\ - tstackh.dat\ - tstacki.dat\ - tstackm.dat + stack.DAT\ + miscloop.DAT\ + dangle.DAT\ + loop.DAT\ + int11.DAT\ + int21.DAT\ + int22.DAT\ + tloop.DAT\ + tstackh.DAT\ + tstacki.DAT\ + tstacke.DAT\ + tstackm.DAT EXTRA_DIST = $(gtfold_data_DATA) CLEANFILES = *~ diff --git a/gtfold-mfe/data/Turner99/asint1x2.dat b/gtfold-mfe/data/Turner99/base_data/asint1x2.dat similarity index 100% rename from gtfold-mfe/data/Turner99/asint1x2.dat rename to gtfold-mfe/data/Turner99/base_data/asint1x2.dat diff --git a/gtfold-mfe/data/Turner99/coaxial.dat b/gtfold-mfe/data/Turner99/base_data/coaxial.dat similarity index 100% rename from gtfold-mfe/data/Turner99/coaxial.dat rename to gtfold-mfe/data/Turner99/base_data/coaxial.dat diff --git a/gtfold-mfe/data/Turner99/coaxstack.dat b/gtfold-mfe/data/Turner99/base_data/coaxstack.dat similarity index 100% rename from gtfold-mfe/data/Turner99/coaxstack.dat rename to gtfold-mfe/data/Turner99/base_data/coaxstack.dat diff --git a/gtfold-mfe/data/Turner99/dangle.dat b/gtfold-mfe/data/Turner99/base_data/dangle.dat similarity index 100% rename from gtfold-mfe/data/Turner99/dangle.dat rename to gtfold-mfe/data/Turner99/base_data/dangle.dat diff --git a/gtfold-mfe/data/Turner99/int11.dat b/gtfold-mfe/data/Turner99/base_data/int11.dat similarity index 100% rename from gtfold-mfe/data/Turner99/int11.dat rename to gtfold-mfe/data/Turner99/base_data/int11.dat diff --git a/gtfold-mfe/data/Turner99/int21.dat b/gtfold-mfe/data/Turner99/base_data/int21.dat similarity index 100% rename from gtfold-mfe/data/Turner99/int21.dat rename to gtfold-mfe/data/Turner99/base_data/int21.dat diff --git a/gtfold-mfe/data/Turner99/int22.dat b/gtfold-mfe/data/Turner99/base_data/int22.dat similarity index 100% rename from gtfold-mfe/data/Turner99/int22.dat rename to gtfold-mfe/data/Turner99/base_data/int22.dat diff --git a/gtfold-mfe/data/Turner99/loop.dat b/gtfold-mfe/data/Turner99/base_data/loop.dat similarity index 100% rename from gtfold-mfe/data/Turner99/loop.dat rename to gtfold-mfe/data/Turner99/base_data/loop.dat diff --git a/gtfold-mfe/data/Turner99/miscloop.dat b/gtfold-mfe/data/Turner99/base_data/miscloop.dat similarity index 100% rename from gtfold-mfe/data/Turner99/miscloop.dat rename to gtfold-mfe/data/Turner99/base_data/miscloop.dat diff --git a/gtfold-mfe/data/Turner99/sint2.dat b/gtfold-mfe/data/Turner99/base_data/sint2.dat similarity index 100% rename from gtfold-mfe/data/Turner99/sint2.dat rename to gtfold-mfe/data/Turner99/base_data/sint2.dat diff --git a/gtfold-mfe/data/Turner99/sint4.dat b/gtfold-mfe/data/Turner99/base_data/sint4.dat similarity index 100% rename from gtfold-mfe/data/Turner99/sint4.dat rename to gtfold-mfe/data/Turner99/base_data/sint4.dat diff --git a/gtfold-mfe/data/Turner99/stack.dat b/gtfold-mfe/data/Turner99/base_data/stack.dat similarity index 100% rename from gtfold-mfe/data/Turner99/stack.dat rename to gtfold-mfe/data/Turner99/base_data/stack.dat diff --git a/gtfold-mfe/data/Turner99/tloop.dat b/gtfold-mfe/data/Turner99/base_data/tloop.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tloop.dat rename to gtfold-mfe/data/Turner99/base_data/tloop.dat diff --git a/gtfold-mfe/data/Turner99/triloop.dat b/gtfold-mfe/data/Turner99/base_data/triloop.dat similarity index 100% rename from gtfold-mfe/data/Turner99/triloop.dat rename to gtfold-mfe/data/Turner99/base_data/triloop.dat diff --git a/gtfold-mfe/data/Turner99/tstack.dat b/gtfold-mfe/data/Turner99/base_data/tstack.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tstack.dat rename to gtfold-mfe/data/Turner99/base_data/tstack.dat diff --git a/gtfold-mfe/data/Turner99/tstackcoax.dat b/gtfold-mfe/data/Turner99/base_data/tstackcoax.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tstackcoax.dat rename to gtfold-mfe/data/Turner99/base_data/tstackcoax.dat diff --git a/gtfold-mfe/data/Turner99/tstackh.dat b/gtfold-mfe/data/Turner99/base_data/tstackh.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tstackh.dat rename to gtfold-mfe/data/Turner99/base_data/tstackh.dat diff --git a/gtfold-mfe/data/Turner99/tstacki.dat b/gtfold-mfe/data/Turner99/base_data/tstacki.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tstacki.dat rename to gtfold-mfe/data/Turner99/base_data/tstacki.dat diff --git a/gtfold-mfe/data/Turner99/tstackm.dat b/gtfold-mfe/data/Turner99/base_data/tstackm.dat similarity index 100% rename from gtfold-mfe/data/Turner99/tstackm.dat rename to gtfold-mfe/data/Turner99/base_data/tstackm.dat diff --git a/gtfold-mfe/data/Turner99/dangle.DAT b/gtfold-mfe/data/Turner99/dangle.DAT new file mode 100644 index 0000000..9fb7c28 --- /dev/null +++ b/gtfold-mfe/data/Turner99/dangle.DAT @@ -0,0 +1,8 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -0.50 -0.80 -0.60 +inf inf inf inf inf inf inf inf -1.70 -0.80 -1.70 -1.20 inf inf inf inf +inf inf inf inf -1.10 -0.40 -1.30 -0.60 inf inf inf inf -0.80 -0.50 -0.80 -0.60 +-0.70 -0.10 -0.70 -0.10 inf inf inf inf -0.70 -0.10 -0.70 -0.10 inf inf inf inf +inf inf inf inf inf inf inf inf inf inf inf inf -0.30 -0.10 -0.20 -0.20 +inf inf inf inf inf inf inf inf -0.20 -0.30 -0.0 -0.0 inf inf inf inf +inf inf inf inf -0.50 -0.30 -0.20 -0.10 inf inf inf inf -0.30 -0.10 -0.20 -0.20 +-0.30 -0.30 -0.40 -0.20 inf inf inf inf -0.30 -0.30 -0.40 -0.20 inf inf inf inf diff --git a/gtfold-mfe/data/Turner99/int11.DAT b/gtfold-mfe/data/Turner99/int11.DAT new file mode 100644 index 0000000..96eabfd --- /dev/null +++ b/gtfold-mfe/data/Turner99/int11.DAT @@ -0,0 +1,24 @@ +1.70 1.70 1.70 1.70 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.10 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 1.70 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b/gtfold-mfe/data/Turner99/int21.DAT @@ -0,0 +1,96 @@ +3.90 3.70 3.10 5.50 3.20 3.00 2.40 4.80 3.20 3.00 2.40 4.80 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 3.90 3.70 3.10 5.50 +3.80 3.70 5.50 3.70 3.10 3.00 4.80 3.00 3.10 3.00 4.80 3.00 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 3.80 3.70 5.50 3.70 +3.20 5.50 2.30 5.50 2.50 4.80 1.60 4.80 2.50 4.80 1.60 4.80 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 3.20 5.50 2.30 5.50 +5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 +3.60 3.20 3.10 5.50 2.90 2.50 2.40 4.80 2.90 2.50 2.40 4.80 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 3.60 3.20 3.10 5.50 +3.70 4.00 5.50 3.70 3.00 3.30 4.80 3.00 3.00 3.30 4.80 3.00 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 3.70 4.00 5.50 3.70 +5.50 5.50 5.50 5.50 4.80 4.80 4.80 4.80 4.80 4.80 4.80 4.80 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 5.50 +5.50 3.70 5.50 2.80 4.80 3.00 4.80 2.10 4.80 3.00 4.80 2.10 5.50 3.70 5.50 2.80 5.50 3.70 5.50 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inf +1.85 1.85 1.85 1.15 inf inf inf inf 1.85 1.85 1.85 1.15 inf inf inf inf diff --git a/gtfold-mfe/data/UNAParams/tstackm.DAT b/gtfold-mfe/data/UNAParams/tstackm.DAT new file mode 100644 index 0000000..ee473db --- /dev/null +++ b/gtfold-mfe/data/UNAParams/tstackm.DAT @@ -0,0 +1,16 @@ +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -1.00 -0.80 -0.90 +inf inf inf inf inf inf inf inf inf inf inf inf -0.60 -0.70 -2.20 -0.70 +inf inf inf inf inf inf inf inf inf inf inf inf -0.80 -2.10 -0.80 -0.80 +inf inf inf inf inf inf inf inf inf inf inf inf -1.10 -0.80 -1.10 -0.80 +inf inf inf inf inf inf inf inf -1.70 -1.70 -1.70 -1.70 inf inf inf inf +inf inf inf inf inf inf inf inf -1.00 -1.10 -3.30 -0.80 inf inf inf inf +inf inf inf inf inf inf inf inf -1.70 -2.40 -1.70 -1.70 inf inf inf inf +inf inf inf inf inf inf inf inf -1.60 -1.40 -1.60 -1.20 inf inf inf inf +inf inf inf inf -1.10 -1.50 -1.30 -1.90 inf inf inf inf -0.80 -1.00 -0.80 -1.30 +inf inf inf inf -1.10 -0.70 -3.40 -0.50 inf inf inf inf -0.60 -0.70 -2.50 -0.70 +inf inf inf inf -1.60 -3.30 -1.40 -1.30 inf inf inf inf -0.80 -2.10 -0.80 -0.80 +inf inf inf inf -1.70 -1.00 -2.00 -0.70 inf inf inf inf -1.40 -0.80 1.30 -0.80 +-1.00 -0.80 -1.10 -1.30 inf inf inf inf -1.00 -0.80 -1.10 -1.00 inf inf inf inf +-0.70 -0.60 -2.40 -0.50 inf inf inf inf -0.70 -0.60 -1.50 -0.50 inf inf inf inf +-1.10 -2.10 -1.20 -1.00 inf inf inf inf -0.70 -1.40 -0.80 0.30 inf inf inf inf +-0.90 -0.60 -1.40 -0.50 inf inf inf inf -0.50 -0.60 -0.50 -0.50 inf inf inf inf diff --git a/gtfold-mfe/depcomp b/gtfold-mfe/depcomp old mode 100644 new mode 100755 index e5f9736..df8eea7 --- a/gtfold-mfe/depcomp +++ b/gtfold-mfe/depcomp @@ -1,10 +1,10 @@ #! /bin/sh # depcomp - compile a program generating dependencies as side-effects -scriptversion=2007-03-29.01 +scriptversion=2009-04-28.21; # UTC -# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007 Free Software -# Foundation, Inc. +# Copyright (C) 1999, 2000, 2003, 2004, 2005, 2006, 2007, 2009 Free +# Software Foundation, Inc. # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -17,9 +17,7 @@ scriptversion=2007-03-29.01 # GNU General Public License for more details. # You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA -# 02110-1301, USA. +# along with this program. If not, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a @@ -87,6 +85,15 @@ if test "$depmode" = dashXmstdout; then depmode=dashmstdout fi +cygpath_u="cygpath -u -f -" +if test "$depmode" = msvcmsys; then + # This is just like msvisualcpp but w/o cygpath translation. + # Just convert the backslash-escaped backslashes to single forward + # slashes to satisfy depend.m4 + cygpath_u="sed s,\\\\\\\\,/,g" + depmode=msvisualcpp +fi + case "$depmode" in gcc3) ## gcc 3 implements dependency tracking that does exactly what @@ -192,14 +199,14 @@ sgi) ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' | \ tr ' -' ' ' >> $depfile - echo >> $depfile +' ' ' >> "$depfile" + echo >> "$depfile" # The second pass generates a dummy entry for each header file. tr ' ' ' ' < "$tmpdepfile" \ | sed -e 's/^.*\.o://' -e 's/#.*$//' -e '/^$/ d' -e 's/$/:/' \ - >> $depfile + >> "$depfile" else # The sourcefile does not contain any dependencies, so just # store a dummy comment line, to avoid errors with the Makefile @@ -328,7 +335,12 @@ hp2) if test -f "$tmpdepfile"; then sed -e "s,^.*\.[a-z]*:,$object:," "$tmpdepfile" > "$depfile" # Add `dependent.h:' lines. - sed -ne '2,${; s/^ *//; s/ \\*$//; s/$/:/; p;}' "$tmpdepfile" >> "$depfile" + sed -ne '2,${ + s/^ *// + s/ \\*$// + s/$/:/ + p + }' "$tmpdepfile" >> "$depfile" else echo "#dummy" > "$depfile" fi @@ -404,7 +416,7 @@ dashmstdout) # Remove the call to Libtool. if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift @@ -455,32 +467,39 @@ makedepend) "$@" || exit $? # Remove any Libtool call if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift fi # X makedepend shift - cleared=no - for arg in "$@"; do + cleared=no eat=no + for arg + do case $cleared in no) set ""; shift cleared=yes ;; esac + if test $eat = yes; then + eat=no + continue + fi case "$arg" in -D*|-I*) set fnord "$@" "$arg"; shift ;; # Strip any option that makedepend may not understand. Remove # the object too, otherwise makedepend will parse it as a source file. + -arch) + eat=yes ;; -*|$object) ;; *) set fnord "$@" "$arg"; shift ;; esac done - obj_suffix="`echo $object | sed 's/^.*\././'`" + obj_suffix=`echo "$object" | sed 's/^.*\././'` touch "$tmpdepfile" ${MAKEDEPEND-makedepend} -o"$obj_suffix" -f"$tmpdepfile" "$@" rm -f "$depfile" @@ -500,7 +519,7 @@ cpp) # Remove the call to Libtool. if test "$libtool" = yes; then - while test $1 != '--mode=compile'; do + while test "X$1" != 'X--mode=compile'; do shift done shift @@ -538,13 +557,27 @@ cpp) msvisualcpp) # Important note: in order to support this mode, a compiler *must* - # always write the preprocessed file to stdout, regardless of -o, - # because we must use -o when running libtool. + # always write the preprocessed file to stdout. "$@" || exit $? + + # Remove the call to Libtool. + if test "$libtool" = yes; then + while test "X$1" != 'X--mode=compile'; do + shift + done + shift + fi + IFS=" " for arg do case "$arg" in + -o) + shift + ;; + $object) + shift + ;; "-Gm"|"/Gm"|"-Gi"|"/Gi"|"-ZI"|"/ZI") set fnord "$@" shift @@ -557,16 +590,23 @@ msvisualcpp) ;; esac done - "$@" -E | - sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::echo "`cygpath -u \\"\1\\"`":p' | sort | uniq > "$tmpdepfile" + "$@" -E 2>/dev/null | + sed -n '/^#line [0-9][0-9]* "\([^"]*\)"/ s::\1:p' | $cygpath_u | sort -u > "$tmpdepfile" rm -f "$depfile" echo "$object : \\" > "$depfile" - . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s:: \1 \\:p' >> "$depfile" echo " " >> "$depfile" - . "$tmpdepfile" | sed 's% %\\ %g' | sed -n '/^\(.*\)$/ s::\1\::p' >> "$depfile" + sed < "$tmpdepfile" -n -e 's% %\\ %g' -e '/^\(.*\)$/ s::\1\::p' >> "$depfile" rm -f "$tmpdepfile" ;; +msvcmsys) + # This case exists only to let depend.m4 do its work. It works by + # looking at the text of this script. This case will never be run, + # since it is checked for above. + exit 1 + ;; + none) exec "$@" ;; @@ -585,5 +625,6 @@ exit 0 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/gtfold-mfe/gtfold_config.h b/gtfold-mfe/gtfold_config.h index 56549bc..b4a21e7 100644 --- a/gtfold-mfe/gtfold_config.h +++ b/gtfold-mfe/gtfold_config.h @@ -53,16 +53,16 @@ #define PACKAGE_NAME "gtfold" /* Define to the full name and version of this package. */ -#define PACKAGE_STRING "gtfold 1.18" +#define PACKAGE_STRING "gtfold 2.0" /* Define to the one symbol short name of this package. */ #define PACKAGE_TARNAME "gtfold" /* Define to the home page for this package. */ -#define PACKAGE_URL "" +/* #undef PACKAGE_URL */ /* Define to the version of this package. */ -#define PACKAGE_VERSION "1.18" +#define PACKAGE_VERSION "2.0" /* Define to 1 if you have the ANSI C header files. */ #define STDC_HEADERS 1 @@ -74,7 +74,7 @@ /* #undef TM_IN_SYS_TIME */ /* Version number of package */ -#define VERSION "1.18" +#define VERSION "2.0" /* Define to empty if `const' does not conform to ANSI C. */ /* #undef const */ diff --git a/gtfold-mfe/include/Makefile.am b/gtfold-mfe/include/Makefile.am index d900fc0..5a61bdd 100644 --- a/gtfold-mfe/include/Makefile.am +++ b/gtfold-mfe/include/Makefile.am @@ -1,3 +1,2 @@ -noinst_HEADERS = algorithms.h algorithms-partition.h constants.h data.h loader.h main-c.h main.h traceback.h - +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h global.h options.h random-sample.h subopt_traceback.h constraints.h energy.h shapereader.h utils.h CLEANFILES = *~ diff --git a/gtfold-mfe/include/Makefile.in b/gtfold-mfe/include/Makefile.in index d049bac..607786e 100644 --- a/gtfold-mfe/include/Makefile.in +++ b/gtfold-mfe/include/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -93,7 +93,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -155,7 +154,7 @@ target_vendor = @target_vendor@ top_build_prefix = @top_build_prefix@ top_builddir = @top_builddir@ top_srcdir = @top_srcdir@ -noinst_HEADERS = algorithms.h algorithms-partition.h constants.h data.h loader.h main-c.h main.h traceback.h +noinst_HEADERS = algorithms.h constants.h data.h loader.h main.h traceback.h partition-dangle.h random-sample.h algorithms-partition.h global.h options.h random-sample.h subopt_traceback.h constraints.h energy.h shapereader.h utils.h CLEANFILES = *~ all: all-am diff --git a/gtfold-mfe/include/algorithms-partition.h b/gtfold-mfe/include/algorithms-partition.h index b45d656..3bfb26d 100644 --- a/gtfold-mfe/include/algorithms-partition.h +++ b/gtfold-mfe/include/algorithms-partition.h @@ -5,25 +5,23 @@ #ifdef __cplusplus extern "C" { #endif - - +/* +typedef struct _pFuncData { + int len; + double** QB; + double** Q; + double** QM; +} p_func_data; +*/ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM); -void fillBasePairProbabilities(int length, int *structure, double **Q, double **QB, double **QM, double**P); -void printBasePairProbabilities(int n, int *structure, double **P); +void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, double**P); +void printBasePairProbabilities(int n, int *structure, double **P, const char* bppfile); double probabilityUnpaired(int length, int i, double **P); double **mallocTwoD(int r, int c); void freeTwoD(double** arr, int r, int c); -typedef struct _pFuncData { - int len; - double** QB; - double** Q; - double** QM; - - // TODO: probability function stuff here -} pFuncData; #ifdef __cplusplus diff --git a/gtfold-mfe/include/algorithms.h b/gtfold-mfe/include/algorithms.h index d919ed1..1f0f1df 100644 --- a/gtfold-mfe/include/algorithms.h +++ b/gtfold-mfe/include/algorithms.h @@ -20,56 +20,15 @@ #ifndef _ALGORITHMS_H #define _ALGORITHMS_H -#include "main-c.h" - -#define MIN(X,Y) ((X) < (Y) ? (X) : (Y)) -#define MAX(X,Y) ((X) > (Y) ? (X) : (Y)) - -/* It returns zero if (i,j) can not make a base pair otherwise return 1. The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). Note that the following condition results into 1 for the allowed base pairs .*/ -#define checkPair(i, j) (((((i)-(j)) % 2) == 1 || (((i)-(j)) % 2)== -1) && (!( ((i)==BASE_A && (j)==BASE_C) || ((i)==BASE_C && (j)==BASE_A) ))) -/* Non GC penalty or AU penalty. Returns a constant penalty if the base pair is not GC or CG */ -#define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0) - -extern int *constraints; - -#ifdef __cplusplus -extern "C" { -#endif - void initTables(int len); - - void init_chPair(); - int update_chPair(int i, int j); -#ifdef __cplusplus -} -#endif - #ifdef __cplusplus extern "C" { #endif - int calculate(int len, int **forceList, int **prohibitList, int forcelen, - int prohibitlen); - - int eS(int i, int j); - int eH(int i, int j); - int eL(int i, int j, int ip, int jp); - -extern enum BOOL NOISOLATE; + int calculate(int len);//, int nThreads, int unamode ,int t_mismatch); #ifdef __cplusplus } #endif -int checkSS(int i, int j); - -void calcVBI(int i, int j); -void calcVM(int i, int j); void calcWM(int i, int j); void calcW(int j); - -void calcVWM(int i, int j, int vbiij, int vmij); void calcVBIVMVWM(int i, int j); -void calcVBIVMVWM2(int i, int j); - -void calcVBIS(int i, int j); -void calcVMVWM(int i, int j); #endif - diff --git a/gtfold-mfe/include/boltzmann_main.h b/gtfold-mfe/include/boltzmann_main.h new file mode 100644 index 0000000..50841d4 --- /dev/null +++ b/gtfold-mfe/include/boltzmann_main.h @@ -0,0 +1,6 @@ +#ifndef _BPP_MAIN_H_ +#define _BPP_MAIN_H_ + +int boltzmann_main(int argc, char** argv); + +#endif diff --git a/gtfold-mfe/include/commented_constants.txt b/gtfold-mfe/include/commented_constants.txt new file mode 100644 index 0000000..a2566c0 --- /dev/null +++ b/gtfold-mfe/include/commented_constants.txt @@ -0,0 +1,51 @@ +typedef struct{ + int poppen[5];/*asymmetric internal loops + From miscloop.dat file: + the f(m) array (see Ninio for details)*/ + int maxpen; /* From miscloop.dat file: + asymmetric internal loops: the ninio equation + the maximum correction*/ + int eparam[11]; /* Amrita: I am not sure of what does this array contain at different values.*/ + /*They seem to be local values used in assignments + Perhaps they should simply be local variables -Anderson*/ + int mult_const[3];/*Multiloop constants + mult_const[0] = a, the penalty for starting a multiloop + mult_const[1] = c, the free base penalty for a multiloop + mult_const[2] = b, the helix penalty for a multiloop*/ + int dangle[4][4][4][2]; /* Dangling energies */ + int inter[31]; /* Size penalty for internal loops */ + int bulge[31]; /* Size penalty for bulges*/ + int hairpin[31]; /* Size penalty for hairpin loops */ + int stack[256]; /* Stacking energy for stack loops */ + int tstkh[256]; /* Terminal stacking energy for hairpin loops */ + int tstki[256]; /* Terminal stacking energy for internal loops */ + int tloop[MAX_T_LOOP + 1][2]; /*MAX_T_LOOP is a constants, should + be the number of Tetraloops we have data for*/ + int num_of_t_loops; /*Should also be a local variable, used as a counter*/ + int iloop22[5][5][5][5][5][5][5][5]; /* 2*1 internal loops*/ + int iloop21[5][5][5][5][5][5][5]; /* 2*1 internal loops */ + int iloop11[5][5][5][5][5][5]; /*1*1 internal loops */ + int coax[6][6][6][6];/*Assumed to be coaxial stacking constants*/ + int tstackcoax[6][6][6][6];/*They are unused by gtfold as of Jan 27 2011*/ + int coax_stack[6][6][6][6];/*Unless functionality is added they should + probably be REMOVED*/ + int tstack[6][6][6][6];/*Unused in loader should probably be REMOVED*/ + int tstkm[6][6][6][6];/*Same as above*/ + + int auend; /* For AU penalty */ + int gubonus; /*GGG hairpin bonus*/ + int cint; /* cint, cslope, c3 are used for poly C hairpin loops */ + int cslope;/*c hairpin slope*/ + int c3;/*CCC hairpin*/ + int efn2a; /*Obsoleted constants should be REMOVED*/ + int efn2b; + int efn2c; + int triloop[MAX_T_LOOP + 1][2];/*Unused in loader should be REMOVED*/ + int num_of_triloops; /*Unused in loader should be REMOVED*/ + int init;/*Intermolecular initiation free energy*/ + bool gail;/*Grossly Asymmetric Interior Loop Rule*/ + float prelog; /* Used for loops having size > 30 */ +}thermo_struct; + + +thermo_struct* populate(char* data_dir); diff --git a/gtfold-mfe/include/constants.h b/gtfold-mfe/include/constants.h index 04eace4..c86d702 100644 --- a/gtfold-mfe/include/constants.h +++ b/gtfold-mfe/include/constants.h @@ -37,10 +37,15 @@ #define MAXLOOP 30 /* The maximum loop size. */ #define MAXENG 1000 +#define TURN 3 #define BASE_A 0 #define BASE_C 1 #define BASE_G 2 #define BASE_U 3 + +#define SUCCESS 1 +#define FAILURE 0 + #endif diff --git a/gtfold-mfe/include/constraints.h b/gtfold-mfe/include/constraints.h new file mode 100644 index 0000000..f21e115 --- /dev/null +++ b/gtfold-mfe/include/constraints.h @@ -0,0 +1,46 @@ +#ifndef _CONSTRAINTS_H_ +#define _CONSTRAINTS_H_ + +extern int* BP; +extern int** PBP; +extern int** FBP; +extern int* ind; + +extern int nPBP; +extern int nFBP; + +//static int load_constraints(const char* constr_file, int verbose=0); + +#define BP(i,j) BP[ind[j]+i] + + +int init_constraints(const char* constr_file, int length) ; +void free_constraints(int length) ; +void print_constraints(int length) ; + +#ifdef __cplusplus +extern "C" { +#endif +int canStack(int i, int j); +int canSS(int i); +int canSSregion(int i, int j); +int canHairpin(int i, int j); +int canILoop(int i, int j, int p, int q); + +int forceSS(int i); +int forceSSregion(int i, int j); +int forcePair(int i, int j); + + +int withinCD(int i, int j); +int verify_structure(); + +void enable_constraints(int b); +void enable_limit_distance(int b); +void set_contact_distance(int dist); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/gtfold-mfe/include/data.h b/gtfold-mfe/include/data.h index 10fcc41..c0875eb 100644 --- a/gtfold-mfe/include/data.h +++ b/gtfold-mfe/include/data.h @@ -32,15 +32,9 @@ extern int dangle[4][4][4][2]; /* Contain dangling energy values */ extern int inter[31]; /* Contains size penalty for internal loops */ extern int bulge[31]; /* Contain the size penalty for bulges */ extern int hairpin[31]; /* Contains the size penalty for hairpin loops */ -#if 0 -extern int stack[4][4][4][4]; -extern int tstkh[4][4][4][4]; -extern int tstki[4][4][4][4]; -#else extern int stack[256]; /* Stacking energy used to calculate energy of stack loops */ extern int tstkh[256]; /* Terminal mismatch energy used in the calculations of hairpin loops */ extern int tstki[256]; /* Terminal mismatch energy used in the calculations of internal loops */ -#endif extern int tloop[maxtloop + 1][2]; extern int numoftloops; extern int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */ @@ -65,5 +59,12 @@ extern int init; extern int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */ extern float prelog; +extern int tstackm[5][5][6][6]; +extern int tstacke[5][5][6][6]; +extern int tstacki23[5][5][5][5]; + + +#define fourBaseIndex(a, b, c, d) (((a) << 6) + ((b) << 4) + ((c) << 2) + (d)) + #endif diff --git a/gtfold-mfe/include/energy.h b/gtfold-mfe/include/energy.h new file mode 100644 index 0000000..30d3fd3 --- /dev/null +++ b/gtfold-mfe/include/energy.h @@ -0,0 +1,53 @@ +#ifndef _ENERGY_TABLES_H_ +#define _ENERGY_TABLES_H_ + +#include "data.h" + +extern int *V; +extern int *W; +extern int *VBI; +extern int *VM; +extern int **WM; +extern int **WMPrime; +extern int *indx; +extern int **PP; + +#define V(i,j) V[indx[j]+i] +#define VM(i,j) VM[indx[j]+i] +#define WM(i,j) WM[i][j] +#define WMPrime(i,j) WMPrime[i][j] +#define WMU(i,j) WM[i][j] +#define WML(i,j) WM[j][i] +#define VBI(i,j) VBI[indx[j]+i] +//#define RT ((0.00198721 * 310.15) * 100.00) +extern const float RT; +extern const float RT_; + +#define auPen(i, j) ((( (i)==BASE_U || (j)==BASE_U ) && ( (i)==BASE_A || (i)==BASE_G || (j)==BASE_A || (j)==BASE_G )) ? auend : 0) + +#ifdef __cplusplus +extern "C" { +#endif +int Ed3(int i, int j, int k); +int Ed5(int i, int j, int k); +int auPenalty(int i, int j); + +#define Ec multConst[1] +#define Eb multConst[2] +#define Ea multConst[0] + +int eS(int i, int j); +int eH(int i, int j); +int eL(int i, int j, int ip, int jp); +int eL1(int i, int j, int ip, int jp); +int Estackm(int i, int j); +int Estacke(int i, int j); + +void create_tables(int len); +void init_tables(int len); +void free_tables(int len); +#ifdef __cplusplus +} +#endif + +#endif diff --git a/gtfold-mfe/include/global.h b/gtfold-mfe/include/global.h new file mode 100644 index 0000000..23ec167 --- /dev/null +++ b/gtfold-mfe/include/global.h @@ -0,0 +1,52 @@ +#ifndef _GLOBAL_H_ +#define _GLOBAL_H_ + +#include "constants.h" + +#ifdef __cplusplus +#include +using namespace std; +#endif + +extern unsigned char *RNA; +extern int *structure; +extern int* constraints; + +extern int g_nthreads; +extern int g_unamode; +extern int g_dangles; +extern int g_mismatch; +extern int g_verbose; +extern int g_prefilter_mode; +extern int g_prefilter1; +extern int g_prefilter2; + +extern unsigned int chPairKey; + +// The possible base pairs are (A,U), (U,A), (C,G), (G,C), (G,U) +// and (U,G). +#define checkPair(i, j) (((((i)-(j)) % 2) == 1 || (((i)-(j)) % 2)== -1) && (!( ((i)==BASE_A && (j)==BASE_C) || ((i)==BASE_C && (j)==BASE_A) ))) + +#ifdef __cplusplus +extern "C" { +#endif +int canPair(int a, int b); +void init_global_params(int len); +void free_global_params(); +void print_sequence(int len); +void print_structure(int len); +void print_header() ; +#ifdef __cplusplus +} +#endif + +#ifdef __cplusplus +int read_sequence_file(const char* filename, std::string& seq); +bool encodeSequence(string seq); +void save_ct_file(string outputFile, string seq, int energy) ; +#endif + +void init_checkPair(); +int update_checkPair(int i, int j); + +#endif diff --git a/gtfold-mfe/include/loader.h b/gtfold-mfe/include/loader.h index ed24d7a..1bac05c 100644 --- a/gtfold-mfe/include/loader.h +++ b/gtfold-mfe/include/loader.h @@ -17,31 +17,30 @@ along with this program. If not, see . */ -/* This file externs the prototypes of functions defined in loader.cc*/ - #ifndef _LOADER_H #define _LOADER_H -#include -#include -#include -#include #include + #include "constants.h" #include "data.h" -void populate(const char *userdatadir,bool userdatalogic); -unsigned char getBase(std::string base); -unsigned char getBase1(std::string base); -int initStackValues(std::string fileName); -int initMiscloopValues(std::string fileName); -int initDangleValues(std::string fileName); -int initLoopValues(std::string fileName); -int initTstkhValues(std::string fileName); -int initTstkiValues(std::string fileName); -int initTloopValues(std::string fileName); -int initInt21Values(std::string fileName); -int initInt22Values(std::string fileName); -int initInt11Values(std::string fileName); +void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode, int rnamode, int t_mismatch); + +int initStackValues(const std::string& fileName, const std::string& dirPath); +int initMiscloopValues(const std::string& fileName, const std::string& dirPath); +int initDangleValues(const std::string& fileName, const std::string& dirPath); +int initLoopValues(const std::string& fileName, const std::string& dirPath); +int initTstkhValues(const std::string& fileName, const std::string& dirPath); +int initTstkiValues(const std::string& fileName, const std::string& dirPath); +int initTloopValues(const std::string& fileName, const std::string& dirPath); +int initInt21Values(const std::string& fileName, const std::string& dirPath); +int initInt22Values(const std::string& fileName, const std::string& dirPath); +int initInt11Values(const std::string& fileName, const std::string& dirPath); +int initTstkmValues(const std::string& fileName, const std::string& dirPath); +int initTstkeValues(const std::string& fileName, const std::string& dirPath); +int initTstk23Values(const std::string& fileName, const std::string& dirPath); + +extern std::string EN_DATADIR; #endif diff --git a/gtfold-mfe/include/main-c.h b/gtfold-mfe/include/main-c.h index 013a553..f56f853 100644 --- a/gtfold-mfe/include/main-c.h +++ b/gtfold-mfe/include/main-c.h @@ -21,7 +21,6 @@ #define _MAIN_C_H extern int LENGTH; -extern unsigned char *RNA1; /* [LENGTH] */ extern unsigned char *RNA; /* [LENGTH] */ extern int *structure; /* [LENGTH] */ extern int *V; /* [(LENGTH-1)*(LENGTH)/2 + 1] */ @@ -38,8 +37,6 @@ enum BOOL { FALSE=0, TRUE }; -extern enum BOOL ILSA; -extern enum BOOL VERBOSE; #define fourBaseIndex(a, b, c, d) (((a) << 6) + ((b) << 4) + ((c) << 2) + (d)) diff --git a/gtfold-mfe/include/main.h b/gtfold-mfe/include/main.h index 8e42832..8fe342e 100644 --- a/gtfold-mfe/include/main.h +++ b/gtfold-mfe/include/main.h @@ -27,24 +27,13 @@ using namespace std; -enum {FAILURE = 0, SUCCESS, NO_CONS_FOUND, ERR_OPEN_FILE}; +//void init_fold(string seq); +//void free_fold(int len); -int initialize_constraints(int*** fbp, int*** pbp, - int& numpConstraints, int& numfConstraints, - const char* constr_file, enum BOOL verbose=FALSE); - -int handle_IUPAC_code(const std::string& s, const int bases); +//bool encodeSequence(string seq); void limit_contact_distance(int lCD, int length); -//void force_noncanonical_basepair(const char* nc_basepairs, int length); - -bool is_valid_base(char c) -{ - return ( (c-'A' == 0) || (c-'a' == 0) || - (c-'C' == 0) || (c-'c' == 0) || - (c-'G' == 0) || (c-'g' == 0) || - (c-'U' == 0) || (c-'u' == 0)); -} +/* void trim_spaces(std::string& str) { // Trim Both leading and trailing spaces @@ -52,13 +41,12 @@ void trim_spaces(std::string& str) size_t endpos = str.find_last_not_of(" \t"); // Find the first character position from reverse af // if all spaces or empty return an empty string - if(( string::npos == startpos ) || ( string::npos == endpos)) + if(( std::string::npos == startpos ) || ( std::string::npos == endpos)) { str = ""; } else str = str.substr( startpos, endpos-startpos+1 ); - } void tokenize(const std::string& str, std::vector& tokens, const std::string& delimiters = " ") @@ -78,8 +66,5 @@ void tokenize(const std::string& str, std::vector& tokens, const st pos = str.find_first_of(delimiters, lastPos); } } - - - - + */ #endif diff --git a/gtfold-mfe/include/mfe_main.h b/gtfold-mfe/include/mfe_main.h new file mode 100644 index 0000000..683be07 --- /dev/null +++ b/gtfold-mfe/include/mfe_main.h @@ -0,0 +1,8 @@ +#ifndef _MFE_MAIN_H_ +#define _MFE_MAIN_H_ + +int mfe_main(int argc, char** argv); +void init_fold(const char* seq); +void free_fold(int len); + +#endif diff --git a/gtfold-mfe/include/options.h b/gtfold-mfe/include/options.h new file mode 100644 index 0000000..a1ecd7a --- /dev/null +++ b/gtfold-mfe/include/options.h @@ -0,0 +1,56 @@ +#ifndef _OPTIONS_H_ +#define _OPTIONS_H_ + +#include +#include +#include +#include + +using namespace std; + +//extern bool ILSA; +//extern bool NOISOLATE; +//extern bool USERDATA; +//extern bool PARAMS; +/* +extern bool LIMIT_DISTANCE; +extern bool BPP_ENABLED; +extern bool SUBOPT_ENABLED; +extern bool CONS_ENABLED; +extern bool VERBOSE; +extern bool SHAPE_ENABLED; +extern bool PARAM_DIR; +extern bool T_MISMATCH; +extern bool UNAMODE; +extern bool RNAMODE; +extern bool CALC_PART_FUNC; +extern bool RND_SAMPLE; +extern bool PF_COUNT_MODE; + +extern string seqfile; +extern string constraintsFile; +extern string shapeFile; +extern string outputDir; +extern string outputFile; +extern string bppOutFile; +extern string suboptFile; +extern string paramDir; + +extern float suboptDelta; +extern int nThreads; +extern bool b_prefilter; +extern int prefilter1; +extern int prefilter2; +extern int dangles; +extern int num_rnd; + +extern bool LIMIT_DISTANCE; +extern int contactDistance; +*/ + +//void help(); +//void parse_options(int argc, char** argv); +//void printRunConfiguration(string seq); + + +#endif diff --git a/gtfold-mfe/include/partition-dangle.h b/gtfold-mfe/include/partition-dangle.h new file mode 100644 index 0000000..2843a60 --- /dev/null +++ b/gtfold-mfe/include/partition-dangle.h @@ -0,0 +1,27 @@ +#ifndef _PARTITION_DANGLE_H +#define _PARTITION_DANGLE_H + +#ifdef __cplusplus +extern "C" { +#endif + +typedef struct partition_d{ + double ** u; + double ** up; + double ** upm; + double ** s1; + double ** s2; + double ** s3; + double ** u1; + int length; +}dangle_struct; + +double cond_dangle(int j, int h, int l); +dangle_struct malloc_partition_arrays_d(int len); +void fill_partition_arrays_d(dangle_struct part_struct); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/gtfold-mfe/include/partition-func.h b/gtfold-mfe/include/partition-func.h new file mode 100644 index 0000000..e9bdffa --- /dev/null +++ b/gtfold-mfe/include/partition-func.h @@ -0,0 +1,40 @@ +#ifndef _PARTITION_DANGLE_H +#define _PARTITION_DANGLE_H + + +#include + +#ifdef __cplusplus +extern "C" { +#endif + +extern double ** u; +extern double ** up; +extern double ** upm; +extern double ** ud; +extern double ** u1d; + +extern double ** s1; +extern double ** s2; +extern double ** s3; +extern double ** u1; + +extern int part_len; +double ED3_new(int i, int j, int k); +double ED5_new(int i, int j, int k); +double EA_new(); +double EB_new(); +double EC_new(); +double eS_new(int i, int j); +double eL_new(int i, int j, int p, int q); +double eH_new(int i, int j); +double auPenalty_new(int i, int j); +double f(int j, int h, int l); +double calculate_partition(int len, int pf_count_mode); +void free_partition(); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/gtfold-mfe/include/random-sample.h b/gtfold-mfe/include/random-sample.h new file mode 100644 index 0000000..4a68889 --- /dev/null +++ b/gtfold-mfe/include/random-sample.h @@ -0,0 +1,15 @@ +#ifndef _RANDOM_SAMPLE_H +#define _RANDOM_SAMPLE_H + +#include + +using namespace std; + +typedef struct sub_seq_t{ + int start; + int end; + int paired; +}sub_seq; + +void multi_loop_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack); +#endif diff --git a/gtfold-mfe/include/shapereader.h b/gtfold-mfe/include/shapereader.h new file mode 100644 index 0000000..02c3a2b --- /dev/null +++ b/gtfold-mfe/include/shapereader.h @@ -0,0 +1,23 @@ +#ifndef _SHAPEREADER_H_ +#define _SHAPEREADER_H_ + +extern double* SHAPEarray; +extern int* SHAPEenergies; + +void readSHAPEarray(const char* filename, int seqlength); +void free_shapeArray(int len); +void print_shapeArray(int len); +int calcShapeEnergy(double shapeNumber); +double shapeModel(double SHAPE_value); + +#ifdef __cplusplus +extern "C"{ +#endif + +int getShapeEnergy(int position); + +#ifdef __cplusplus +} +#endif + +#endif diff --git a/gtfold-mfe/include/stochastic-sampling.h b/gtfold-mfe/include/stochastic-sampling.h new file mode 100644 index 0000000..38f037f --- /dev/null +++ b/gtfold-mfe/include/stochastic-sampling.h @@ -0,0 +1,88 @@ +#ifndef __STOCHASTIC_SAMPLING__ +#define __STOCHASTIC_SAMPLING__ + +#include +#include +#include "partition-func.h" +#include "energy.h" + +enum {U=0,UP,UD,U1,U1D}; + +double randdouble(); +double U_0(int i, int j); +double U_ij(int i, int j); +double U_hj(int i, int h, int j); +double U_il(int i, int j); +double U_s1h(int i, int h, int j); +double U_ihlj_case1(int i, int h, int l, int j); +double U_ihlj_case2(int i, int h, int l, int j); +double U_ihlj_case3(int i, int h, int l, int j); +double UD_il_case1(int i, int l, int j); +double UD_il_case2(int i, int l, int j); +double UD_il_case3(int i, int l, int j); +double Q_ijH(int i, int j); +double Q_ijS(int i, int j); +double Q_ijM(int i, int j); +double UPM_ip1l_case1(int i, int l, int j); +double UPM_ip1l_case2(int i, int l, int j); +double UPM_ip2l_case1(int i, int l , int j); +double UPM_ip2l_case2(int i, int l , int j); +double UPM_ijs2h(int i, int h , int j); +double UPM_ijhl_case1(int i, int h, int l, int j); +double UPM_ijhl_case2(int i, int h, int l, int j); +double U1D_ij_il_case1(int i, int l, int j); +double U1D_ij_il_case2(int i, int l, int j); +double U1D_ij_il_case3(int i, int l, int j); +double U1_ij(int i, int j); +double U1_ij_s3h(int i, int h, int j); +double U1_j_hl_case1(int h, int l, int j); +double U1_j_hl_case2(int h, int l, int j); +double U1_j_hl_case3(int h, int l, int j); + +struct base_pair +{ + int i; + int j; + int t; + + base_pair(int i_, int j_, int t_) : i(i_), j(j_), t(t_) {} + base_pair(const base_pair& bp) :i(bp.i), j(bp.j), t(bp.t) { } + base_pair& operator = (const base_pair& bp) + { + if (this != &bp) + { + i = bp.i; + j = bp.j; + t = bp.t; + } + return *this; + } + + int type() const { return t ;} + + bool isPaired() const + { + return t == UP; + } + + friend std::ostream& operator << (std::ostream& out, const base_pair& bp) + { + out << '(' << bp.i << '-' << bp.j << ')' << ' ' << bp.t << std::endl; + return out; + } +}; + +void set_single_stranded(int i, int j, int* structure); +void set_base_pair(int i, int j, int* structure); + +void rnd_upm(int i, int j, int* structure); +void rnd_u1d(int i, int j, int* structure) ; +void rnd_u1(int i, int j, int* structure); +void rnd_up(int i, int j, int* structure); +void rnd_ud(int i, int j, int* structure); +void rnd_u(int i, int j, int* structure); + +double rnd_structure(int* structure, int len); +void batch_sample(int num_rnd, int length, double U); + +#endif diff --git a/gtfold-mfe/include/subopt_main.h b/gtfold-mfe/include/subopt_main.h new file mode 100644 index 0000000..1f26e43 --- /dev/null +++ b/gtfold-mfe/include/subopt_main.h @@ -0,0 +1,6 @@ +#ifndef _SUBOPT_MAIN_H_ +#define _SUBOPT_MAIN_H_ + +int subopt_main(int argc, char** argv); + +#endif diff --git a/gtfold-mfe/include/subopt_traceback.h b/gtfold-mfe/include/subopt_traceback.h index 00cbc8c..2ab2241 100644 --- a/gtfold-mfe/include/subopt_traceback.h +++ b/gtfold-mfe/include/subopt_traceback.h @@ -30,18 +30,9 @@ #include #include +#define UNIQUE_MULTILOOP_DECOMPOSITION -#define Ed3(x, y, z) dangle[RNA[x]][RNA[y]][RNA[z]][1] -#define Ed5(x, y, z) dangle[RNA[x]][RNA[y]][RNA[z]][0] -#define auPenalty(x, y) auPen(RNA[x], RNA[y]) -#define Ea multConst[0] -#define Eb multConst[2] -#define Ec multConst[1] - -#define V(x,y) V[indx[x]+y] -#define TURN 3 - -enum label {lW=0, lV, lVBI, lVM, lWM}; +enum label {lW=0, lV, lVBI, lVM, lWM, lWMPrime, lM, lM1}; extern const char* lstr[]; struct segment @@ -188,7 +179,7 @@ struct pstruct return st_v.empty(); } - void print() + void print() const { SEGSTACK st = st_segment; std::cout <<'[' << ' ' ; @@ -228,10 +219,17 @@ void push_to_gstack(ps_stack_t & gs, const ps_t& v); ss_map_t subopt_traceback(int len, int gap); -void traceV(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceW(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs, int energy); -void traceWM(ps_t& ps, ps_map_t& filter); +void traceV(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceVBI(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceW(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceVM(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceWM(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceWMPrime(int i, int j, ps_t & ps, ps_stack_t & gs); +//void traceWM(ps_t& ps, ps_map_t& filter); + +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION +void traceM(int i, int j, ps_t & ps, ps_stack_t & gs); +void traceM1(int i, int j, ps_t & ps, ps_stack_t & gs); +#endif #endif diff --git a/gtfold-mfe/include/traceback.h b/gtfold-mfe/include/traceback.h index bfe96f0..ff654f4 100644 --- a/gtfold-mfe/include/traceback.h +++ b/gtfold-mfe/include/traceback.h @@ -26,7 +26,7 @@ #ifdef __cplusplus extern "C" { #endif - void trace(int len); + void trace(int len); //, int vv, int mode, int mismatch); #ifdef __cplusplus } #endif @@ -36,5 +36,6 @@ int traceV(int i, int j); int traceVM(int i, int j); int traceVBI(int i, int j); int traceWM(int i, int j); +int traceWMPrime(int i, int j); #endif diff --git a/gtfold-mfe/include/utils-c.h b/gtfold-mfe/include/utils-c.h new file mode 100644 index 0000000..92b3d32 --- /dev/null +++ b/gtfold-mfe/include/utils-c.h @@ -0,0 +1,5 @@ +#ifndef _UTILS-C_H_ +#define _UTILS-C_H_ + + +#endif diff --git a/gtfold-mfe/include/utils.h b/gtfold-mfe/include/utils.h new file mode 100644 index 0000000..a8e5c28 --- /dev/null +++ b/gtfold-mfe/include/utils.h @@ -0,0 +1,21 @@ +#ifndef _UTILS_H_ +#define _UTILS_H_ + +#include "constants.h" + +#define MIN(X,Y) ((X) < (Y) ? (X) : (Y)) +#define MAX(X,Y) ((X) > (Y) ? (X) : (Y)) +#define MIN4(W,X,Y,Z) MIN(MIN(W,X),MIN(Y,Z)) +#define MIN3(W,X,Y) MIN(MIN(W,X),Y) + +char baseToDigit(const char* base) ; +unsigned char encode(char base); +int isWatsonCrickBase(char base); +double get_seconds(); + +#ifdef __cplusplus +extern "C" +#endif +int is_valid_base(char c); + +#endif diff --git a/gtfold-mfe/install-sh b/gtfold-mfe/install-sh index a5897de..6781b98 100755 --- a/gtfold-mfe/install-sh +++ b/gtfold-mfe/install-sh @@ -1,7 +1,7 @@ #!/bin/sh # install - install a program, script, or datafile -scriptversion=2006-12-25.00 +scriptversion=2009-04-28.21; # UTC # This originates from X11R5 (mit/util/scripts/install.sh), which was # later released in X11R6 (xc/config/util/install.sh) with the @@ -515,5 +515,6 @@ done # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/gtfold-mfe/missing b/gtfold-mfe/missing old mode 100644 new mode 100755 index 1c8ff70..28055d2 --- a/gtfold-mfe/missing +++ b/gtfold-mfe/missing @@ -1,10 +1,10 @@ #! /bin/sh # Common stub for a few missing GNU programs while installing. -scriptversion=2006-05-10.23 +scriptversion=2009-04-28.21; # UTC -# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006 -# Free Software Foundation, Inc. +# Copyright (C) 1996, 1997, 1999, 2000, 2002, 2003, 2004, 2005, 2006, +# 2008, 2009 Free Software Foundation, Inc. # Originally by Fran,cois Pinard , 1996. # This program is free software; you can redistribute it and/or modify @@ -18,9 +18,7 @@ scriptversion=2006-05-10.23 # GNU General Public License for more details. # You should have received a copy of the GNU General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA -# 02110-1301, USA. +# along with this program. If not, see . # As a special exception to the GNU General Public License, if you # distribute this file as part of a program that contains a @@ -89,6 +87,9 @@ Supported PROGRAM values: tar try tar, gnutar, gtar, then tar without non-portable flags yacc create \`y.tab.[ch]', if possible, from existing .[ch] +Version suffixes to PROGRAM as well as the prefixes \`gnu-', \`gnu', and +\`g' are ignored when checking the name. + Send bug reports to ." exit $? ;; @@ -106,15 +107,22 @@ Send bug reports to ." esac +# normalize program name to check for. +program=`echo "$1" | sed ' + s/^gnu-//; t + s/^gnu//; t + s/^g//; t'` + # Now exit if we have it, but it failed. Also exit now if we # don't have it and --version was passed (most likely to detect -# the program). +# the program). This is about non-GNU programs, so use $1 not +# $program. case $1 in - lex|yacc) + lex*|yacc*) # Not GNU programs, they don't have --version. ;; - tar) + tar*) if test -n "$run"; then echo 1>&2 "ERROR: \`tar' requires --run" exit 1 @@ -138,7 +146,7 @@ esac # If it does not exist, or fails to run (possibly an outdated version), # try to emulate it. -case $1 in +case $program in aclocal*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if @@ -148,7 +156,7 @@ WARNING: \`$1' is $msg. You should only need it if touch aclocal.m4 ;; - autoconf) + autoconf*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified \`${configure_ac}'. You might want to install the @@ -157,7 +165,7 @@ WARNING: \`$1' is $msg. You should only need it if touch configure ;; - autoheader) + autoheader*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified \`acconfig.h' or \`${configure_ac}'. You might want @@ -187,7 +195,7 @@ WARNING: \`$1' is $msg. You should only need it if while read f; do touch "$f"; done ;; - autom4te) + autom4te*) echo 1>&2 "\ WARNING: \`$1' is needed, but is $msg. You might have modified some files without having the @@ -210,7 +218,7 @@ WARNING: \`$1' is needed, but is $msg. fi ;; - bison|yacc) + bison*|yacc*) echo 1>&2 "\ WARNING: \`$1' $msg. You should only need it if you modified a \`.y' file. You may need the \`Bison' package @@ -240,7 +248,7 @@ WARNING: \`$1' $msg. You should only need it if fi ;; - lex|flex) + lex*|flex*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a \`.l' file. You may need the \`Flex' package @@ -263,7 +271,7 @@ WARNING: \`$1' is $msg. You should only need it if fi ;; - help2man) + help2man*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a dependency of a manual page. You may need the @@ -277,11 +285,11 @@ WARNING: \`$1' is $msg. You should only need it if else test -z "$file" || exec >$file echo ".ab help2man is required to generate this page" - exit 1 + exit $? fi ;; - makeinfo) + makeinfo*) echo 1>&2 "\ WARNING: \`$1' is $msg. You should only need it if you modified a \`.texi' or \`.texinfo' file, or any other file @@ -310,7 +318,7 @@ WARNING: \`$1' is $msg. You should only need it if touch $file ;; - tar) + tar*) shift # We have already tried tar in the generic part. @@ -363,5 +371,6 @@ exit 0 # eval: (add-hook 'write-file-hooks 'time-stamp) # time-stamp-start: "scriptversion=" # time-stamp-format: "%:y-%02m-%02d.%02H" -# time-stamp-end: "$" +# time-stamp-time-zone: "UTC" +# time-stamp-end: "; # UTC" # End: diff --git a/gtfold-mfe/scripts/dats2DATs.py b/gtfold-mfe/scripts/dats2DATs.py new file mode 100755 index 0000000..e488b84 --- /dev/null +++ b/gtfold-mfe/scripts/dats2DATs.py @@ -0,0 +1,53 @@ +import os, sys, re + +# read in arguments from command line +if len(sys.argv) != 3: + print "need directory names" + print "Usage: dats2DATs.py " +source_dir_name = sys.argv[1] +target_dir_name = sys.argv[2] + +# this function opens a .dat formatted file and returns a string with .DAT file format +def dat2DAT(file_name, num_cols, num_rows): + num_data_rows_seen = 0 + DAT_content = "" + file = open(file_name,'r') + + for line in file.readlines() : + if re.match('[\d\-\.\s]+\n', line) and not re.match('[\s\-]*\n', line): + # If the line contains only digits, negative signs, dots, and white space + # and does not contain ony dashes and whitespace convert the line to .DAT format + DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line) + DAT_line = re.sub('\s+\-','\t-', DAT_line) + DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line) + DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line) + DAT_line = DAT_line.lstrip().rstrip()+"\n" + DAT_content += DAT_line + + return DAT_content + +for file_prefix in ["dangle", "int11", "int21", "int22", "loop", "miscloop", "sint2", "sint4", "stack", "tstackh", "tstacki", "tstackm"]: + file_name = source_dir_name+"/"+file_prefix+".dat" + output_file_path = target_dir_name+"/"+file_prefix+".DAT" + output_file = open(output_file_path, 'w') + output_file.write(dat2DAT(file_name, 16, 16)) + #print dat2DAT(file_name, 16, 16) + +file_name = source_dir_name+"/tloop.dat" +output_file_path = target_dir_name+"/tloop.DAT" +DAT_content = "" +file = open(file_name,'r') + +for line in file.readlines() : + if re.match('[\d\-\.\sACGU]+\n', line) and not re.match('[\s\-]*\n', line): + # If the line contains only digits, negative signs, dots, and white space or ACGU + # and does not contain ony dashes and whitespace convert the line to .DAT format + DAT_line = re.sub('\s+\.(\s)',r'\tinf\1', line) + DAT_line = re.sub('\s+\-','\t-', DAT_line) + DAT_line = re.sub('\s+(\d)',r'\t\1', DAT_line) + DAT_line = re.sub('\s+(\.\d)',r'\t\1', DAT_line) + DAT_line = DAT_line.lstrip().rstrip()+"\n" + DAT_content += DAT_line +output_file = open(output_file_path, 'w') +output_file.write(DAT_content) + diff --git a/gtfold-mfe/src/Makefile.am b/gtfold-mfe/src/Makefile.am index 49f310e..8a1ba22 100644 --- a/gtfold-mfe/src/Makefile.am +++ b/gtfold-mfe/src/Makefile.am @@ -7,12 +7,23 @@ bin_PROGRAMS = gtfold gtfold_SOURCES = \ main.cc\ - loader.cc\ - subopt_traceback.cc\ + mfe_main.cc\ + loader.cc\ + utils.cc\ + options.cc\ + constraints.cc\ + global.cc\ + energy.c\ algorithms.c\ - algorithms-partition.c\ - traceback.c - + traceback.c\ + subopt_main.cc\ + subopt_traceback.cc\ + stochastic-sampling.cc\ + algorithms-partition.c\ + boltzmann_main.cc\ + partition-dangle.c\ + partition-func.c\ + shapereader.cc gtfold_LDFLAGS = diff --git a/gtfold-mfe/src/Makefile.in b/gtfold-mfe/src/Makefile.in index b3a8a1a..86a7787 100644 --- a/gtfold-mfe/src/Makefile.in +++ b/gtfold-mfe/src/Makefile.in @@ -1,4 +1,4 @@ -# Makefile.in generated by automake 1.11.1 from Makefile.am. +# Makefile.in generated by automake 1.11 from Makefile.am. # @configure_input@ # Copyright (C) 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, @@ -31,7 +31,7 @@ PRE_INSTALL = : POST_INSTALL = : NORMAL_UNINSTALL = : PRE_UNINSTALL = : -POST_UNINSTALL = : +POST_UNINSTALL = : build_triplet = @build@ host_triplet = @host@ target_triplet = @target@ @@ -48,9 +48,13 @@ CONFIG_CLEAN_FILES = CONFIG_CLEAN_VPATH_FILES = am__installdirs = "$(DESTDIR)$(bindir)" PROGRAMS = $(bin_PROGRAMS) -am_gtfold_OBJECTS = main.$(OBJEXT) loader.$(OBJEXT) \ - subopt_traceback.$(OBJEXT) algorithms.$(OBJEXT) \ - algorithms-partition.$(OBJEXT) traceback.$(OBJEXT) +am_gtfold_OBJECTS = main.$(OBJEXT) mfe_main.$(OBJEXT) loader.$(OBJEXT) \ + utils.$(OBJEXT) options.$(OBJEXT) constraints.$(OBJEXT) \ + global.$(OBJEXT) energy.$(OBJEXT) algorithms.$(OBJEXT) \ + traceback.$(OBJEXT) subopt_main.$(OBJEXT) \ + subopt_traceback.$(OBJEXT) stochastic-sampling.$(OBJEXT) \ + algorithms-partition.$(OBJEXT) boltzmann_main.$(OBJEXT) partition-dangle.$(OBJEXT) \ + partition-func.$(OBJEXT) shapereader.$(OBJEXT) gtfold_OBJECTS = $(am_gtfold_OBJECTS) gtfold_DEPENDENCIES = gtfold_LINK = $(CXXLD) $(AM_CXXFLAGS) $(CXXFLAGS) $(gtfold_LDFLAGS) \ @@ -114,7 +118,6 @@ PACKAGE_BUGREPORT = @PACKAGE_BUGREPORT@ PACKAGE_NAME = @PACKAGE_NAME@ PACKAGE_STRING = @PACKAGE_STRING@ PACKAGE_TARNAME = @PACKAGE_TARNAME@ -PACKAGE_URL = @PACKAGE_URL@ PACKAGE_VERSION = @PACKAGE_VERSION@ PATH_SEPARATOR = @PATH_SEPARATOR@ SET_MAKE = @SET_MAKE@ @@ -181,11 +184,23 @@ AM_CFLAGS = $(OPENMP_CFLAGS) -DDATADIR='$(datadir)/@PACKAGE@' AM_CXXFLAGS = -DDATADIR='$(datadir)/@PACKAGE@' gtfold_SOURCES = \ main.cc\ - loader.cc\ - subopt_traceback.cc\ + mfe_main.cc\ + loader.cc\ + utils.cc\ + options.cc\ + constraints.cc\ + global.cc\ + energy.c\ algorithms.c\ - algorithms-partition.c\ - traceback.c + traceback.c\ + subopt_main.cc\ + subopt_traceback.cc\ + stochastic-sampling.cc\ + algorithms-partition.c\ + boltzmann_main.cc\ + partition-dangle.c\ + partition-func.c\ + shapereader.cc gtfold_LDFLAGS = gtfold_LDADD = -lm @@ -244,8 +259,11 @@ install-binPROGRAMS: $(bin_PROGRAMS) while read type dir files; do \ if test "$$dir" = .; then dir=; else dir=/$$dir; fi; \ test -z "$$files" || { \ - echo " $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ + echo "$(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files '$(DESTDIR)$(bindir)$$dir'"; \ $(INSTALL_PROGRAM_ENV) $(INSTALL_PROGRAM) $$files "$(DESTDIR)$(bindir)$$dir" || exit $$?; \ + ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtmfe || exit $$?;\ + ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtsubopt || exit $$?;\ + ln -sf $$files $(DESTDIR)$(bindir)$$dir/gtboltzmann || exit $$?;\ } \ ; done @@ -272,11 +290,23 @@ distclean-compile: -rm -f *.tab.c @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms-partition.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/boltzmann_main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/algorithms.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/constraints.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/energy.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/global.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/loader.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/main.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/mfe_main.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/options.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-dangle.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/partition-func.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/shapereader.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/stochastic-sampling.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_main.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/subopt_traceback.Po@am__quote@ @AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/traceback.Po@am__quote@ +@AMDEP_TRUE@@am__include@ @am__quote@./$(DEPDIR)/utils.Po@am__quote@ .c.o: @am__fastdepCC_TRUE@ $(COMPILE) -MT $@ -MD -MP -MF $(DEPDIR)/$*.Tpo -c -o $@ $< diff --git a/gtfold-mfe/src/algorithms-partition.c b/gtfold-mfe/src/algorithms-partition.c index 0a1f5ac..fa3b9b8 100644 --- a/gtfold-mfe/src/algorithms-partition.c +++ b/gtfold-mfe/src/algorithms-partition.c @@ -4,9 +4,18 @@ #include #include "algorithms.h" +#include "utils.h" +#include "energy.h" +#include "global.h" #include "algorithms-partition.h" #include "data.h" +#ifdef _OPENMP +#include "omp.h" +#endif + + +#define MAX_LOOP 30 // double[][] QB; // double[][] Q; @@ -14,7 +23,6 @@ // Boltzmann constant (R) * Standard 37C temperature (T in Kelvin) -double RT = 0.00198721 * 310.15; // Based on pseudocode in figure 6 in // @@ -29,7 +37,9 @@ double RT = 0.00198721 * 310.15; * @param QM Matrix * */ -void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { + + +void fill_partition_fn_arrays(int len, double** Q, double** QB, double** QM) { // multiConst[3] is a global variable with 3 values: a, b, c for the // experimental constants @@ -55,28 +65,45 @@ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { // fill in values in the array for(l=1; l<=len; ++l) { - for(i=1; i<= len-l+1; ++i) { + //Parrallelize + //#ifdef _OPENMP + //#pragma omp parallel for private (i,j) schedule(guided) + //#endif + for(i=1; i<= len - l + 1; i++) { - int j = i+l-1; + int j = i + l - 1; // QB recursion // Only calculate if i and j actually pair - if(checkPair(i,j)) { + if(canPair(RNA[i],RNA[j])) { // NOTE: eH returns an integer encoded as fixed point. So a // return value of 115 represents raw value 115/100 = 1.15 - QB[i][j] = exp(-eH(i,j)/100.0/RT); - + QB[i][j] = exp(-eH(i,j)/RT); + for(d=i+1; d<=j-4; ++d) { + //if(d - i - 1 > MAX_LOOP) + // break; for(e=d+4; e<=j-1; ++e) { - - if(d == i + 1 && e == j -1) - QB[i][j] += exp(-eS(i,j)/100.0/RT)*QB[d][e]; - else - QB[i][j] += exp(-eL(i,j,d,e)/100.0/RT)*QB[d][e]; - - QB[i][j] += QM[i+1][d-1]*QB[d][e] * - exp(-(a + b + c*(j-e-1))/100.0/RT); + + // if(d - i - 1 + j - e - 1 > MAX_LOOP) + // break; + + if(QB[d][e] != 0){ + //more general than chkpair + //if we cant pair, move on + + if(d == i + 1 && e == j -1){ + QB[i][j] += exp(-eS(i,j)/RT)*QB[d][e]; + } + else{ + //printf("i: %d j: %d d: %d e: %d\n", i,j,d,e); + QB[i][j] += exp(-eL(i,j,d,e)/RT)*QB[d][e]; + } + + QB[i][j] += QM[i+1][d-1]*QB[d][e] * + exp(-(a + b + c*(j-e-1))/RT); + } } } } @@ -86,12 +113,13 @@ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { for(d=i; d<=j-4; ++d) { for(e=d+4; e<=j; ++e) { Q[i][j] += Q[i][d-1]*QB[d][e]; - QM[i][j] += exp(-(b+c*(d-i)+c*(j-e))/100.0) * QB[d][e]; - QM[i][j] += QM[i][d-1] * QB[d][e] * exp(-(b+c*(j-e))/100.0/RT); + QM[i][j] += exp(-(b+c*(d-i)+c*(j-e))/RT) * QB[d][e]; + QM[i][j] += QM[i][d-1] * QB[d][e] * exp(-(b+c*(j-e))/RT); } } } } + printf("Total partition number: %f\n", Q[1][len]); } /** @@ -101,7 +129,7 @@ void fill_partition_fn_arrays(int len, double** QB, double** Q, double** QM) { * index j. structure[i] = 0 means the nucleotide is * unpaired. */ -void fillBasePairProbabilities(int length, int *structure, double **Q, double **QB, double **QM, double**P) { +void fillBasePairProbabilities(int length, double **Q, double **QB, double **QM, double**P) { int d, l, h, i, j; double tempBuffer; @@ -135,22 +163,22 @@ void fillBasePairProbabilities(int length, int *structure, double **Q, double ** tempBuffer = P[i][j]*QB[h][l]/QB[i][j]; if(i == h-1 && j == l+1) //of which stacked pairs are a special case - tempBuffer *= exp(-eS(i,j)/100.0/RT); + tempBuffer *= exp(-eS(i,j)/RT); else - tempBuffer *= exp(-eL(i,j,h,l)/100.0/RT); + tempBuffer *= exp(-eL(i,j,h,l)/RT); P[h][l] += tempBuffer; // third term tempBuffer = 0; // Start over for multiloops if(j - l > 3) - tempBuffer += exp(-((h-i-1)*c/100.0/RT)) * QM[l+1][j-1]; + tempBuffer += exp(-((h-i-1)*c/RT)) * QM[l+1][j-1]; if(h - i > 3) - tempBuffer += exp(-((j-l-1)*c/100.0/RT)) * QM[i+1][h-1]; + tempBuffer += exp(-((j-l-1)*c/RT)) * QM[i+1][h-1]; if(j - l > 3 && h - i > 3) tempBuffer += QM[i+1][h-1] * QM[l+1][j-1]; - tempBuffer *= P[i][j] * QB[h][l] / QB[i][j] * exp(-(a+b)/100.0/RT); + tempBuffer *= P[i][j] * QB[h][l] / QB[i][j] * exp(-(a+b)/RT); P[h][l] += tempBuffer; } @@ -171,16 +199,21 @@ void fillBasePairProbabilities(int length, int *structure, double **Q, double ** * unpaired. * @param P Partition function array */ -void printBasePairProbabilities(int n, int *structure, double **P) { +void printBasePairProbabilities(int n, int *structure, double **P, const char* outfile) { + FILE* outp = fopen(outfile,"w"); + if (outp == NULL) { + fprintf(stderr, "printBasePairProbabilities() : Cannot open %s",outfile); + } int i; for(i=1; i<=n; ++i) { int j = structure[i]; if(j) - printf("%d-%d pair\tPr: %f\n", i, j, P[MIN(i,j)][MAX(i,j)]); + fprintf(outp, "%d-%d pair\tPr: %f\n", i, j, P[MIN(i,j)][MAX(i,j)]); else - printf("%d unpaired\tPr: %f\n", i, probabilityUnpaired(n, i, P)); + fprintf(outp, "%d unpaired\tPr: %f\n", i, probabilityUnpaired(n, i, P)); } + fclose(outp); } /** @@ -215,7 +248,6 @@ double **mallocTwoD(int r, int c) { return NULL; } } - return arr; } diff --git a/gtfold-mfe/src/algorithms.c b/gtfold-mfe/src/algorithms.c index 83f94d6..07f987f 100644 --- a/gtfold-mfe/src/algorithms.c +++ b/gtfold-mfe/src/algorithms.c @@ -1,1453 +1,320 @@ /* - GTfold: compute minimum free energy of RNA secondary structure - Copyright (C) 2008 David A. Bader - http://www.cc.gatech.edu/~bader - - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. - - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. - - You should have received a copy of the GNU General Public License - along with this program. If not, see . - */ - -/* AUTHORED by Amrita Mathuriya August 2007 - January 2009. Implemented multiloop energy function, internal loop energy function using heuristic and internal loop speedup algorithm, parallelization, corrected numerous bugs and commented whole GTfold. - - * Amrita: Please note that, in this file same recursion formulas is being calculated in more than one functions. - * This is done for performance improvement to reduce the redundant computations for various cases. The duplicate codes are not documented again at some places. - * The arrays to be calculated are VBI, VM, V and WM for every point (i,j) where j > i. Then W(j) needs to be calculated for j= 1 to N. - * NOTE that the WM(i,j) can be calculated only after V(i,j) and array VBI and VM should be calculated before V array for point (i,j). So, the order of computation has been kept as VBI, VM, V, WM for any point (i,j) - * Also Note that, a valid base pair has j > i. Therefore, the portion of the 2D arrays containing j < i is not useful. - * Minimum size of a hairpin loop is assumed as 3. This assumption is taken into effect at many places. - * I am not sure of what these eparam values are at various places except for multiloops. - * */ - -/* Modified by Sainath Mallidi August 2009 - "*/ -/* Added constraint support that can force a base pair, prohibit a base pair and make single stranded regions */ - +GTfold: compute minimum free energy of RNA secondary structure +Copyright (C) 2008 David A. Bader +http://www.cc.gatech.edu/~bader +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. +You should have received a copy of the GNU General Public License +along with this program. If not, see . + */ #include #include +#include +#include #include -#include "data.h" +#include #include "constants.h" -#include "main-c.h" +#include "utils.h" +#include "energy.h" +#include "global.h" #include "algorithms.h" -#ifdef _OPENMP /* The compiler automatically recognizes openmp support and includes the file accordingly*/ +#include "constraints.h" +#include "shapereader.h" +#ifdef _OPENMP #include "omp.h" #endif -#define DEBUG 0 - -#define WM(i,j) WM[j][i] /* This pragma is defined for readability purpose.*/ - -unsigned int chPairKey; +//#define DEBUG 1 -//Constraint arrays -int plen = 0, flen = 0, sslen = 0; -int *pbpi, *pbpj, *fbpi, *fbpj, *ss; +void initializeMatrix(int len) { + int i, j; -/* This function calculates chPairKey to be processed by function chPair. Defined by Professor Bader. */ -void init_chPair() { - int i, j; - - chPairKey = 0; - for (i = 0; i < 4; i++) - for (j = 0; j < 4; j++) - chPairKey += checkPair(i, j) << ((i << 2) + j); + for (i = 1; i <= len; ++i) + for (j = len; j >= i; --j) + if (canPair(RNA[i],RNA[j]) && j-i > TURN) + PP[i][j] = 1; } -int update_chPair(int i, int j) -{ - int r = 0; - if (!((i >= 0 && i <=3 )&&(j >=0 && j <=3))) - return r; +void prefilter(int len, int prefilter1, int prefilter2) { + char** in; + int i, j, k, count; + + in = (char**)malloc(len*sizeof(char*)); + for (i = 1; i <= len; ++i) in[i - 1] = (char*)malloc(len*sizeof(char)); + + for (i = 1; i <= len - prefilter2 + 1; ++i) + for (j = len; j >= prefilter2 && j >= i; --j) { + count = 0; + for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k) + if (PP[i + k][j - k] == 1) ++count; + if (count >= prefilter1) + for (k = 0; k < prefilter2 && k <= (j - i) / 2; ++k) + ++in[i + k - 1][j - k - 1]; + } - if (!(chPairKey & (1 << ((i << 2) + j)))) - { - chPairKey += 1 << ((i << 2) + j); - r = 1; - } + for (i = 1; i <= len; ++i) { + for (j = len; j >= i; --j) + if (!in[i - 1][j - 1]) PP[i][j] = 0; + free(in[i - 1]); + } - return r; + free(in); } +int calcVBI(int i, int j) { + int p=0, q=0; + int VBIij = INFINITY_; -/* This pragma returns 1 if base b1 and b2 can pair up, otherwise returns 0, using chPairKey calculated in init_chPair function. Here b1 and b2 are 0-3 to represent one of the four nucleotides A, C, G and U. */ -#if 0 -inline -int chPair(int b1, int b2) { - return (chPairKey & (1 << ((b1<<2) + b2))); -} -#else -#define chPair(a, b) (chPairKey & (1 << (((a)<<2) + (b)))) /* Please try to run this, to understand this statement. Defined by Professor Bader. */ -#endif - -/* Initialize variables.*/ -void initTables(int len) { - - int i, j; - int LLL; - -#if 0 - int z = (len)*(len+1)/2 + 1; - - V = new int[z]; - indx = new int[len+1]; -#endif + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); -#if DEBUG - if (len != LENGTH-1) - fprintf(stderr,"ERROR: in initTables, len (%5d) != LENGTH-1 (%5d)\n",len,LENGTH-1); -#endif - - init_chPair(); + for (q = minq; q <= maxq; q++) { + if (PP[p][q]==0) continue; + if (!canILoop(i,j,p,q)) continue; + VBIij = MIN(eL(i, j, p, q) + V(p,q), VBIij); + } + } - for (i = 0; i < LENGTH; i++) { - W[i] = INFINITY_; /* Initializing W array with INFINITY make sure that an unfolded sequence will have a large +ve value for free energy - INIFINITY*/ - constraints[i] = 0; -#if 0 - indx[i] = (LENGTH-1)*(i-1) - (i*(i-1))/2; - indx[i] = (len)*(i-1) - (i*(i-1))/2; -#endif - for (j = 0; j < LENGTH; j++) { - VBI[i][j] = INFINITY_; - VM[i][j] = INFINITY_; - WM[i][j] = INFINITY_; - } - } + return VBIij; +} - LLL = (LENGTH - 1) * (LENGTH) / 2 + 1; +int calcVBI1(int i, int j) { + int p=0, q=0; + int VBIij = INFINITY_; - for (i = 0; i < LLL; i++) - V[i] = INFINITY_; + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); - /*The array V is mapped from 2D to 1D and indexed using the indx array. This mapping helps removing the space wasted for j < i*/ - for (i = 0; i <= LENGTH - 1; i++) - indx[i] = (len) * (i - 1) - (i * (i - 1)) / 2; + for (q = minq; q <= maxq; q++) { + if (PP[p][q]==0) continue; + if (!canILoop(i,j,p,q)) continue; + VBIij = MIN(eL1(i, j, p, q) + V(p,q), VBIij); + } + } - return; + return VBIij; } -//check if single stranded region is allowed with the given constraints -int checkSS(int i, int j) { +int calcVBI2(int i, int j, int len) { + int d, ii, jj; + int energy = INFINITY_; - int it; - for (it = i + 1; it < j; it++) { - if (constraints[it] > 0) - return 1; - } - return 0; + for (d = j-i-3; d >= TURN+1 && d >= j-i-2-MAXLOOP; --d) + for (ii = i + 1; ii < j - d && ii <= len; ++ii) + { + jj = d + ii; + if (PP[ii][jj]==1) + energy = MIN(energy, eL1(i, j, ii, jj) + V(ii, jj)); + } + return energy; } -int calculate(int len, int **forceList, int **prohibitList, int forcelen, int prohibitlen) { - int b, i, j, it, k; - - for(i=1;i<=len;i++) - { - if(RNA1[i]=='N') - constraints[i] = -1; - } - - if (prohibitlen != 0) - { - for (it = 0; it < prohibitlen; it++) - { - for(k= 1; k <= prohibitList[it][2];k++) - { - constraints[prohibitList[it][0]+k-1] = -1; - if(prohibitList[it][1]!=0) - { - constraints[prohibitList[it][1]+1-k] = -1; - } - } - } - } - - if (forcelen != 0) - { - printf("Running with constraints\n"); - for (it = 0; it < forcelen; it++) - { - for(k=1; k <= forceList[it][2];k++) - { - if (!chPair(RNA[forceList[it][0]+k-1], RNA[forceList[it][1]-k+1])) - { - printf("Can't constrain (%d,%d)\n", forceList[it][0]+k-1, - forceList[it][1]-k+1); - continue; - } - constraints[forceList[it][0]+k-1] = forceList[it][1]+1-k; - constraints[forceList[it][1]+1-k] = forceList[it][0]+k-1; - } - //printf("(%d,%d)\n", forceList[it][0], forceList[it][1]); - } - } - +int calculate(int len) { + int b, i, j; #ifdef _OPENMP - if (num_threads > 0) - omp_set_num_threads(num_threads); + if (g_nthreads > 0) omp_set_num_threads(g_nthreads); #endif -#if 1 #ifdef _OPENMP #pragma omp parallel #pragma omp master - { - fprintf(stdout,"Thread count: %3d\n",omp_get_num_threads()); - } + if (g_verbose) fprintf(stdout,"Thread count: %3d \n",omp_get_num_threads()); #endif -#endif - - //printf("starting.......\n"); - /* Here b-1 is the length of the segment closed with (i,j) base pair. We assume the minimum size of a hairpin loop closed with (i,j) equal to 3.*/ - - /* For b = 4 to 6, hairpin loops and at b = 6 stack loops are possible. So, only WM, and V array are needs to be calculated. - * If (i,j) can not pair up then only WM needs to be calculated. - * */ - for (b = 4; b <= 6; b++) { -#ifdef _OPENMP -#pragma omp parallel for private (i,j) schedule(guided) - /* OpenMP syntex to parallelize the for loop. Guided scheduling strategy works better because there may not be equla amount of work for every (i,j) - * Please look at the conference paper on GTfold for information regarding how to parallelize the code. Also, note that the for every value of b calculation has to go sequentially. However, the calculation for a perticular value of b, which corresponds to calculating on a single diagonal. - * */ -#endif - for (i = 1; i <= len - b; i++) { - j = i + b; - //if (constraints[i] == -1 && constraints[j] == -1) - // continue; - if (j-i >= contact_dist) continue; - if (chPair(RNA[i], RNA[j])) /* Check if bases i and j pair up or not */ - calcVWM(i, j, INFINITY_, INFINITY_); /* Calculates V and WM array for element (i,j)*/ - else - calcWM(i, j); /* Calculates WM array for element (i,j)*/ - } - } + initializeMatrix(len); + if (g_unamode || g_prefilter_mode) { + prefilter(len,g_prefilter1,g_prefilter2); + } - /* For b=7 to 10, base pair (i,j) is not able to form multiloops. */ - for (b = 7; b <= 10; b++) { + for (b = TURN+1; b <= len-1; b++) { #ifdef _OPENMP #pragma omp parallel for private (i,j) schedule(guided) #endif - for (i = 1; i <= len - b; i++) { - j = i + b; - //if (constraints[i] == -1 && constraints[j] == -1) - // continue; - if (j-i >= contact_dist) continue; - if (chPair(RNA[i], RNA[j])) { - calcVBI(i, j); /* Calculates VBI element at (i,j) */ - calcVWM(i, j, VBI[i][j], INFINITY_); /* Calculates V and WM arrays*/ - } else - calcWM(i, j); /* Calculates WM element at (i,j) */ + for (i = 1; i <= len - b; i++) { + j = i + b; + + if (PP[i][j] == 1) { + int eh = canHairpin(i,j)?eH(i,j):INFINITY_; //hair pin + int es = canStack(i,j)?eS(i,j)+V(i+1,j-1):INFINITY_; // stack + + // Internal Loop BEGIN + if (g_unamode) + VBI(i,j) = calcVBI1(i,j); + else + VBI(i,j) = calcVBI(i,j); + // Internal Loop END + + // Multi Loop BEGIN + int d3 = canSS(j-1)?Ed3(i,j,j-1):INFINITY_; + int d5 = canSS(i+1)?Ed5(i,j,i+1):INFINITY_; + + if (g_unamode || g_mismatch) { // unamode, terminal mismatch + VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb); + VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-1] + d5 + auPenalty(i,j) + Ea + Eb + Ec); + VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-2] + d3 + auPenalty(i,j) + Ea + Eb + Ec); + VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-2] + Estackm(i,j) + auPenalty(i,j) + Ea + Eb + 2*Ec); + } else if (g_dangles == 2) { // -d2 + VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + d3 + d5 + auPenalty(i,j) + Ea + Eb); + } else if (g_dangles == 0) { // -d0 + VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb); + } else { // default + VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-1] + auPenalty(i,j) + Ea + Eb); + VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-1] + d5 + auPenalty(i,j) + Ea + Eb + Ec); + VM(i,j) = MIN(VM(i,j), WMPrime[i+1][j-2] + d3 + auPenalty(i,j) + Ea + Eb + Ec); + VM(i,j) = MIN(VM(i,j), WMPrime[i+2][j-2] + d3 + d5 + auPenalty(i,j) + Ea + Eb + 2*Ec); } + VM(i,j) = canStack(i,j)?VM(i,j):INFINITY_; + // Multi Loop END + + V(i,j) = MIN4( eh, + es, + VBI(i,j), + VM(i,j)); + } + else { + V(i,j) = INFINITY_; + } + + // Added auxillary storage WMPrime to speedup multiloop calculations + int h; + for (h = i+TURN+1 ; h <= j-TURN-2; h++) { + WMPrime[i][j] = MIN(WMPrime[i][j], WMU(i,h-1) + WML(h,j)); + } + + // WM begin + int newWM = INFINITY_; + + //ZS: This sum corresponds to when i,j are NOT paired with each other. + //So we need to make sure only terms where i,j aren't pairing are considered. + newWM = (!forcePair(i,j))?MIN(newWM, WMPrime[i][j]):newWM; + + if (g_unamode || g_mismatch) { // unamode + newWM = MIN(V(i,j) + auPenalty(i,j) + Eb, newWM); + newWM = canSS(i)?MIN(V(i+1,j) + Ed3(j,i+1,i) + auPenalty(i+1,j) + Eb + Ec, newWM):newWM; //i dangle + newWM = canSS(j)?MIN(V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec, newWM):newWM; //j dangle + if (i= contact_dist) continue; - if (chPair(RNA[i], RNA[j])) { - calcVBIVMVWM(i, j); /* Calculates VBI, VM, V and WM elements at (i,j) */ - } else - calcWM(i, j); /* Calculates WM element at (i,j) */ - } + } + + W[0] = 0; + for (j = 1; j <= len; j++) { + int i, Wj, Widjd, Wijd, Widj, Wij, Wim1; + Wj = 0; + for (i = 1; i < j-TURN; i++) { + Wij = Widjd = Wijd = Widj = INFINITY_; + Wim1 = MIN(0, W[i-1]); + + if (g_unamode || g_mismatch) { // unafold option + Wij = V(i, j) + auPenalty(i, j) + Wim1; + Widj = canSS(i)?V(i+1, j) + auPenalty(i+1,j) + Ed3(j,i + 1,i) + Wim1:Widj; + Wijd = canSS(j)?V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + Wim1:Wijd; + Widjd = (canSS(i)&&canSS(j))?V(i+1,j-1) + auPenalty(i+1,j-1) + Estacke(j-1,i+1) + Wim1:Widjd; + Wij = MIN4(Wij, Widjd, Wijd, Widj); + } else if (g_dangles == 2) { // -d2 option + int energy = V(i,j) + auPenalty(i,j) + Wim1; + if (i>1) energy += Ed3(j,i,i-1); + if (j0; i--){ - printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WM[i][j]); - } + W[j] = canSS(j)?MIN(Wj, W[j-1]):Wj; + } + +#ifdef DEBUG + FILE* file = fopen("VBI.txt", "w"); + int ii, jj; + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,VBI(ii,jj)); } -*/ - - for (j = 5; j <= len; j++) /* Recurssion relation for W array does not depend upon any other array, so can be done after the computation of other arrays are finished.*/ - calcW(j); - - //printV(len); - - return W[len]; -} -/* This function calculates the optimal energy of internal loops closed with base pair (i,j) using a heuristic, which limits their size to a constant value - MAXLOOP - An internal loop contains one closing base pair (i,j) and one enclosed base pair (ip,jp). This function searches for the best enclosed base pair for the closing base pair (i,j) within the given window limited by MAXLOOP - */ -void calcVBI(int i, int j) { - - int ip, jp, temp, VBIij, thres1; - - VBIij = INFINITY_; - - if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0 - && constraints[j] != i) || constraints[i] == -1 || constraints[j] - == -1) - return; - - /* Having ip = i+1 and jp = j-1, creates a stack loop. Stack loops are taken care separately in the calculation of V using eS() function. Therefore, for ip=i+1, the jp value should be lesser than or equal to j-2.*/ - ip = i + 1; - thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of the hairpin loop which the enclosed base pair (ip,jp) can close is 3 that results in the minimum value of jp = ip+4 */ - for (jp = thres1; jp <= j - 2; jp++) { - //May need to check the constraint condition here - if (jp-ip >= contact_dist) continue; - if (chPair(RNA[ip], RNA[jp])) { - if (checkSS(i, ip) || checkSS(jp, j)) - continue; - temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the optimal energy of the substructure closed by (ip,jp)*/ - if (VBIij > temp) - VBIij = temp; - } - } - - for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) { - thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of a hairpin loop is 3, so start jp from ip+4*/ - //May need to check for forced constraints here - for (jp = thres1; jp <= j - 1; jp++) { - if (jp-ip >= contact_dist) continue; - if (chPair(RNA[ip], RNA[jp])) { - if (checkSS(i, ip) || checkSS(jp, j)) - continue; - temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the optimal energy of the substructure closed by (ip,jp)*/ - if (VBIij > temp) - VBIij = temp; - } - } - } - - VBI[i][j] = VBIij; - return; -} - -/* Amrita: - Internal loop speedup algorithm */ -/* Calculation of internal loops using internal loop speedup algorithm. The algorithm calculates the optimal loop closed with base pair (i,j) */ -void calcVBIS(int i, int j) { - - int ip, jp, E, VBIij, c = 3, b, len = LENGTH - 1, E1, E2, g; /* ip and jp form enclosed base pairs and c is a small constant currently taken as 3. The loops having one or both sides smaller than c are calculated as special cases. */ - - if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0 - && constraints[j] != i) || constraints[i] == -1 || constraints[j] - == -1) - return; - - VBIij = VBI[i][j]; - - /*Case1: Loops having first side shorter than c and second side has all allowable sizes */ - /* Having ip = i+1 and jp=j-1 creates a stack which is considered separately in eS function. So here the max value of jp could be j-2*/ - ip = i + 1; - for (jp = ip + 4; jp <= j - 2; jp++) { - if (jp-ip >= contact_dist) continue; - if (chPair(RNA[ip], RNA[jp])) { - E = eL(i, j, ip, jp) + V[indx[ip] + jp]; - if (VBIij > E) - VBIij = E; - } - } - - for (ip = i + 2; ip <= i + c; ip++) { - for (jp = ip + 4; jp <= j - 1; jp++) { /* Minimum size of a hairpin loop is 3.*/ - if (jp-ip >= contact_dist) continue; - if (chPair(RNA[ip], RNA[jp])) { - E = eL(i, j, ip, jp) + V[indx[ip] + jp]; - if (VBIij > E) - VBIij = E; - } - } - } - - /*Case 2: When the first side is greater or equal to c but the second side is smaller */ - for (ip = i + c + 1; ip < j - 1; ip++) { - for (jp = j - c; jp <= j - 1 && jp >= ip + 4; jp++) { /* Minimum size of a hairpin loop is 3.*/ - if (jp-ip >= contact_dist) continue; - if (chPair(RNA[ip], RNA[jp])) { - E = eL(i, j, ip, jp) + V[indx[ip] + jp]; - if (VBIij > E) - VBIij = E; - } - } - } - - /* Case 3: General Case - when both sides of internal loops are greater than or equal to c */ - /*Base cases for this (i,j) are g=j-i-2c-3 and j-i-2c-4, gap values should always be greater than or equal to 3*/ - /* First base case - both sides of the loop are equal to c.*/ - ip = i + c + 1; - jp = j - c - 1; - - g = jp - ip - 1; - if (g < 3) { - VBI[i][j] = VBIij; - return; - } /* if g is lesser than 3, then you don't extend this value. In this case the second base case of g-1=j-i-2c-4 will also not make a valid gap value. */ - - E = eL(i, j, ip, jp) + V[indx[ip] + jp]; - if (VBIij > E) - VBIij = E; - - /* Extend this base case for all closing base pairs of the form ( i-b, j+b ) */ - - for (b = 1; b <= MIN(i - 1, len - j); b++) { - - E = eL(i - b, j + b, ip, jp) + V[indx[ip] + jp]; - - /* Two more options for base pair (i-b,j+b), which are introduced by having one of the side of the resultant internal loop exactly equal to c */ - /* Second side is c - with closing base pair (i-b,j+b)*/ - int ip1 = i + c + 1 + b; - int jp1 = (j + b) - c - 1; - E1 = eL(i - b, j + b, ip1, jp1) + V[indx[ip1] + jp1]; - - /* First side is c - with closing base pair (i-b,j+b)*/ - int ip2 = (i - b) + c + 1; - int jp2 = j - c - 1 - b; - E2 = eL(i - b, j + b, ip2, jp2) + V[indx[ip2] + jp2]; - - if (E > E1) { - E = E1; - ip = ip1; - jp = jp1; - } - if (E > E2) { - E = E2; - ip = ip2; - jp = jp2; - } - if (VBI[i - b][j + b] > E) { - VBI[i - b][j + b] = E; - } - } - - if (g == 3) { - VBI[i][j] = VBIij; - return; - } /* In this case the gap g-1=2, which should not be extended.*/ - ip = i + c + 2; - jp = j - c - 1; - E1 = eL(i, j, ip, jp) + V[indx[ip] + jp]; - E2 = eL(i, j, i + c + 1, j - c - 2) + V[indx[i + c + 1] + j - c - 2]; - if (VBIij > E1) - VBIij = E1; - if (VBIij > E2) - VBIij = E2; - - if (E2 < E1) { - ip = i + c + 1; - jp = j - c - 2; - } - - for (b = 1; b <= MIN(i - 1, len - j); b++) { - E = eL(i - b, j + b, ip, jp) + V[indx[ip] + jp]; - - /*Two more options for base pair (i-b,j+b), having one of the sides equal to c */ - /* First side is equal to c*/ - int ip1 = (i - b) + c + 1; - int jp1 = (j) - c - 2 - b; - E1 = eL(i - b, j + b, ip1, jp1) + V[indx[ip1] + jp1]; - - /* Second side is equal to c*/ - int ip2 = i + c + 2 + b; - int jp2 = (j + b) - c - 1; - E2 = eL(i - b, j + b, ip2, jp2) + V[indx[ip2] + jp2]; - - if (E > E1) { - E = E1; - ip = ip1; - jp = jp1; - } - if (E > E2) { - E = E2; - ip = ip2; - jp = jp2; - } - if (VBI[i - b][j + b] > E) { - VBI[i - b][j + b] = E; - } - } - - VBI[i][j] = VBIij; -} - -/* Function for calculating the value of WM(i,j)*/ -void calcWM(int i, int j) { - - int b = multConst[2], c = multConst[1]; /* b is the branch penalty and c is penalty for single bases for multiloops*/ - int h; - /* WMidjd = dangling base on both ith and jth side. WMidj = dangling base on ith side. WMijd = dangling base on jth side. WMij = no dangling base on both sides */ - int WMidjd, WMidj, WMijd, WMij, WMijp; - int rnai, rnaj; - rnai = RNA[i]; /* Read the value of RNA[i] and RNA[j] in register to make the program execute faster.*/ - rnaj = RNA[j]; - - WMijp = INFINITY_; /* See, the data flow through the function - how it has been calculated. */ - - /* Minimum size of a hairpin loop is 3, that makes the starting limit of h=i+4 and end limit of j-5*/ - for (h = i + 4; h < j - 4; h++) { - int temp = WM[i][h] + WM(h+1,j); - if (temp <= WMijp) - WMijp = temp; - } - - WMidjd = INFINITY_; - WMidj = INFINITY_; - WMijd = INFINITY_; - WMij = INFINITY_; - - /* If base i and j pair up. */ - WMij = V[indx[i] + j] + auPen(rnai, rnaj) + b; - /* If base i+1 and j pair up. Add the dangling interaction energy of base pair (i+1,j) with base i being on the 3' end */ - if (constraints[i] <= 0) - WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen( - RNA[i + 1], rnaj) + b + c; - /* If base i and j-1 pair up. Add the dangling interaction energy of base pair (i,j-1) with base j being on the 5' end */ - if (constraints[j] <= 0) - WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen( - rnai, RNA[j - 1]) + b + c; - /* If base i+1 and j-1 pair up. Add the dangling interaction energy of base pair (i+1,j-1) with base i on the 3' and base j on the 5' end.*/ - if (constraints[i] <= 0 && constraints[j] <= 0) - WMidjd = V[indx[i + 1] + j - 1] - + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1] - + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1], - RNA[j - 1]) + b + 2* c ; - - // if(i==6 && j==11) - // printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d, constraints: (%d,%d)\n", i, j, WMij, WMidj, WMijd, WMidjd, constraints[i], constraints[j]); - - /* Take the minimum of all of the terms */ - WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd)); - - int WMsip1j = INFINITY_; - int WMsijm1 = INFINITY_; - - if (constraints[i] <= 0) - WMsip1j = WM[i + 1][j]; - - if (constraints[j] <= 0) - WMsijm1 = WM[i][j - 1]; - - - WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij); - WMij = MIN(WMijp, WMij); - - //printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij); - - WM[i][j] = WMij; - WM(i,j) = WMij; /* Extra instruction. NOTE that - by having this instruction we are making WM array symmetric. The macro will convert this instruction into WM[j][i] = WM[i][j] making WM array symmetric.*/ - return; -} - -/* Function used for calculating the value of V and WM for a given i,j pair. Calculation of WM at (i,j) requires value of V at (i,j)*/ -void calcVWM(int i, int j, int VBIij, int VMij) { - int a, b, c, h, Vij, eh, es; - int WMidjd, WMidj, WMijd, WMij, WMijp; - int rnai, rnaj; - - rnai = RNA[i]; - rnaj = RNA[j]; - - WMidjd = INFINITY_; - WMidj = INFINITY_; - WMijd = INFINITY_; - WMij = INFINITY_; - - /* V starts */ - eh = eH(i, j); /* Energy of a hairpin loop */ - es = eS(i, j); /* Energy of a stack, with (i,j) and (i-1,j+1) base pairs.*/ - if (es == 0) { - es = INFINITY_; - } else - es += V[indx[i + 1] + j - 1]; - - Vij = MIN(MIN(eh, es), MIN(VBIij, VMij)); - - if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0 - && constraints[j] != i) || constraints[i] == -1 || constraints[j] - == -1) - Vij = INFINITY_; - - // printf("%d, V(%d,%d): eh: %d, es: %d, vbi: %d, vm: %d, v: %d\n", j-i, i, j, eh, es, VBIij, VMij, Vij); - - V[indx[i] + j] = Vij; - - if (NOISOLATE == TRUE && Vij < INFINITY_) { - //Check if i+1,j-1 have paired - if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) { - //If not then check for i-1, j+1 - - //Isolated base pairs look ahead - int eHL = eH(i - 1, j + 1); - int eSL = eS(i - 1, j + 1) + V[indx[i] + j]; - if (i - 1 == 0) { - eSL = 0; - eHL = 0; - } - int Vijl = (eHL < eSL) ? eHL : eSL; - // printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl); - - if (Vijl > INFINITY_ - SMALLINFTY_) - //isolated base pair found.. setting energy to infinity - V[indx[i] + j] = Vij = INFINITY_; - } - } - -#if DEBUG - if (indx[i]+j > (LENGTH-1)*(LENGTH)/2) - fprintf(stderr,"ERROR: in calcVMW: i: %5d j: %5d\n",i,j); -#endif - /* V ends */ - - /* WM starts */ - a = multConst[0]; - b = multConst[2]; - c = multConst[1]; - WMijp = INFINITY_; - - for (h = i + 4; h <= j - 5; h++) { - int temp = WM[i][h] + WM(h+1,j); - if (temp < WMijp) - WMijp = temp; - } - - WMij = Vij + auPen(rnai, rnaj) + b; - - if (constraints[i] <= 0) - WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen( - RNA[i + 1], rnaj) + b + c; - - if (constraints[j] <= 0) - WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen( - rnai, RNA[j - 1]) + b + c; - - if (constraints[i] <= 0 && constraints[j] <= 0) - WMidjd = V[indx[i + 1] + j - 1] - + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1] - + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1], - RNA[j - 1]) + b + 2* c ; - - WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd)); - - int WMsip1j = INFINITY_; - int WMsijm1 = INFINITY_; - - if (constraints[i] <= 0) - WMsip1j = WM[i + 1][j]; - - if (constraints[j] <= 0) - WMsijm1 = WM[i][j - 1]; - - WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij); - WMij = MIN(WMijp, WMij); - - //printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij); - - WM[i][j] = WMij; - WM(i,j) = WMij; /* extra instruction */ - /* WM ends */ - return; -} - -/* Function for calculating VM, V, and WM at point (i,j) in the order . Calculation of V at (i,j) requires VBI and VM. Also, calculation of final value of WM(i,j) requires V at (i,j) */ - -void calcVMVWM(int i, int j) { - - int a = multConst[0] /*offset penalty for multiloops*/, - b = multConst[2]/*penalty per branch for multiloops*/, c = - multConst[1]/* Penalty per single base in the multiloop*/, - a1, h, es; - int aupen; - int WMijp, WMidjd, WMidj, WMijd, WMij; - int VMij, VMijd, VMidj, VMidjd, A_temp; - int WMip1hm1 /* WM value at i+1 and j-1 */, - WMip2hm1/* WM value at i+2 and h-1*/, - WMhjm1/* WM value at h and j-1*/, WMhjm2/* WM value at h and j-2*/, - WMhp1j /*WM value at h+1 and j*/; - int rnai, rnaj; - int tmp1, tmp2; - - rnai = RNA[i]; - rnaj = RNA[j]; - - WMidjd = INFINITY_; - WMidj = INFINITY_; - WMijd = INFINITY_; - WMij = INFINITY_; - - /* VM and WM starts */ - aupen = auPen(rnai, rnaj); /* AU or NON GC penalty for base pair (i,j) */ - VMij = INFINITY_; - VMijd = INFINITY_; - VMidj = INFINITY_; - VMidjd = INFINITY_; - - /* Manoj starts */ - - WMijp = WM[i][i + 4] + WM(i+5,j); - a1 = WM[i][i + 5] + WM(i+6,j); - if (a1 <= WMijp) - WMijp = a1; - - /* Here we are doing the calculation of VM and WM at point (i,j) concurrently. This for loop calculates the values of VMij, VMidj, VMijd, VMidjd with the value of WMijp. The value of WMijp is needed for calculating the value of WM at (i,j). However, it should be noted that the final value of WM[i][j] requires value of V at (i,j) and will be calculated in the end. */ - - /* There are four possibilities for the multiloop closing base pair for the inclusion of dangling energies. - * 1) Including the dangling energy of i+1 base and also for base j-1 with the base pair (i,j) closing the multiloop - VMidjd - * 2) Including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j) - VMidj - * 3) NOT including the danlging energy of i+1 base and including the dangling energy of base j-1 with the closing base pair (i,j) - VMijd - * 4) NOT including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j)-VMij - * */ - for (h = i + 6; h <= j - 5; h++) { - - a1 = WM[i][h]; - WMip1hm1 = WM[i + 1][h - 1]; - WMip2hm1 = WM[i + 2][h - 1]; -#if 0 - WMhjm1 = WM[h][j-1]; - WMhjm2 = WM[h][j-2]; - WMhp1j = WM[h+1][j]; -#else - WMhjm1 = WM(h,j-1); /* Preprocessor will convert this into WM[j-1][h]. According to the algorithm, the expression should be WM[h][j-1] -- in which case, as the value of h changes, this will access elements from a column of the WM matrix. To improve run time performance WM array is made symmetric and so WM[h][j-1] = WM[j-1][h] and it will have accesses in a row.*/ - WMhjm2 = WM(h,j-2); /* Same reason as above */ - WMhp1j = WM(h+1,j); /* Same reason as above */ -#endif - - /* WM starts */ - a1 += WMhp1j; - if (a1 <= WMijp) - WMijp = a1; - /* WM ends */ - - /* Calculation of the four options for VM*/ - A_temp = WMip1hm1 + WMhjm1; - if ((A_temp <= VMij)) - VMij = A_temp; - - A_temp = WMip2hm1 + WMhjm1; - if (A_temp <= VMidj && constraints[i + 1] <= 0) - VMidj = A_temp; - - A_temp = WMip1hm1 + WMhjm2; - if (A_temp <= VMijd && constraints[j - 1] <= 0) - VMijd = A_temp; - - A_temp = WMip2hm1 + WMhjm2; - if (A_temp <= VMidjd && constraints[i + 1] <= 0 && constraints[j - 1] - <= 0) - VMidjd = A_temp; - } - -#if 0 - VMidj += dangle[rnai][rnaj][RNA[i+1]][0]; - VMijd += dangle[rnai][rnaj][RNA[j-1]][1]; - VMidjd += dangle[rnai][rnaj][RNA[i+1]][0] + dangle[rnai][rnaj][RNA[j-1]][1]; -#else - tmp1 = dangle[rnai][rnaj][RNA[i + 1]][0]; /* Dangling energy of base pair (i,j) with single base i+1 at 5' end */ - tmp2 = dangle[rnai][rnaj][RNA[j - 1]][1]; /* Dangling energy of base pair (i,j) with single base j-1 at 3' end */ - VMidj += (tmp1 + c); - VMidjd += (tmp1 + c); - VMijd += (tmp2 + c); - VMidjd += (tmp2 + c); -#endif - - /* Manoj ends */ - - VMij = MIN(MIN(VMij, VMidj), MIN(VMijd, VMidjd)); - VMij = VMij + b + a + aupen; - - if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0 - && constraints[j] != i) || constraints[i] == -1 || constraints[j] - == -1) - VMij = INFINITY_; - - VM[i][j] = VMij; - /* VM ends */ - - /* V starts */ - es = eS(i, j); - if (es == 0) { - es = INFINITY_; - } else - es += V[indx[i + 1] + j - 1]; - - int Vij; - Vij = MIN(MIN(eH(i, j), es), MIN(VBI[i][j], VMij)); - - if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0 - && constraints[j] != i) || constraints[i] == -1 || constraints[j] - == -1) - Vij = INFINITY_; - - V[indx[i] + j] = Vij; - - if (NOISOLATE == TRUE && Vij < INFINITY_) { - //Check if i+1,j-1 have paired - if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) { - //If not then check for i-1, j+1 - - //Isolated base pairs look ahead - int eHL = eH(i - 1, j + 1); - int eSL = eS(i - 1, j + 1) + V[indx[i] + j]; - if (i - 1 == 0) { - eSL = 0; - eHL = 0; - } - int Vijl = (eHL < eSL) ? eHL : eSL; - //printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl); - - if (Vijl > INFINITY_ - SMALLINFTY_) - //isolated base pair found.. setting energy to infinity - V[indx[i] + j] = Vij = INFINITY_; - } - } - -#if DEBUG - if (indx[i]+j > (LENGTH-1)*(LENGTH)/2) - fprintf(stderr,"ERROR: in calcVBIVMVWM: i: %5d j: %5d\n",i,j); -#endif - - /* V ends */ - - /* WM starts */ - - //Need to take care of these WMs - WMij = Vij + auPen(rnai, rnaj) + b; - - if (constraints[i] <= 0) - WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen( - RNA[i + 1], rnaj) + b + c; - - if (constraints[j] <= 0) - WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen( - rnai, RNA[j - 1]) + b + c; - - if (constraints[i] <= 0 && constraints[j] <= 0) - WMidjd = V[indx[i + 1] + j - 1] - + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1] - + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1], - RNA[j - 1]) + b + 2* c ; - - WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd)); - - int WMsip1j = INFINITY_; - int WMsijm1 = INFINITY_; - - if (constraints[i] <= 0) - WMsip1j = WM[i + 1][j]; - - if (constraints[j] <= 0) - WMsijm1 = WM[i][j - 1]; - - WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij); - - //printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij); - - WM[i][j] = MIN(WMijp, WMij); - WM(i,j) = WM[i][j]; /* extra instruction */ - /* WM ends */ - - return; -} - -/* Calculation of VBI, VM, V and WM in the order. Calculation of V at (i,j) requires VBI and VM. Also, calculation of final value of WM(i,j) requires V at (i,j) */ -void calcVBIVMVWM(int i, int j) { - - int ip, jp, temp, VBIij, thres1; - int - a = multConst[0] /*a is an offset penalty for multiloops */, - b = multConst[2]/* b is penalty for multiloop branches, one per branch*/, - c = multConst[1] /*Penalty for single stranded nucleotides in the multiloops*/, - a1, h, es; - int aupen; - int WMijp, WMidjd, WMidj, WMijd, WMij; - int VMij, VMijd, VMidj, VMidjd, A_temp; - int WMip1hm1 /* WM value at i+1 and h-1 */, - WMip2hm1 /* WM value at i+2 and j-1*/, - WMhjm1 /*WM value at h and j-1*/, - WMhjm2 /* WM value at h and j-2*/, WMhp1j /*WM value at h+1 and j*/; - int rnai, rnaj; - int tmp1, tmp2; - - rnai = RNA[i]; - rnaj = RNA[j]; - - WMidjd = INFINITY_; - WMidj = INFINITY_; - WMijd = INFINITY_; - WMij = INFINITY_; - - /* VBI starts */ - /* Look at the calcVBI function for explanation of internal loop calculations*/ - VBIij = INFINITY_; - - int ifinal, jfinal; - /* ip=i+1, jp=j-1 closes a stack, so we should set the jp limit till j-2, in the following loop*/ - ip = i + 1; - thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); /* Minimum size of a hairpin loop is 3. So, start jp from ip+4 */ - for (jp = thres1; jp <= j - 2; jp++) { - if (jp-ip >= contact_dist) continue; - if (chPair(RNA[ip], RNA[jp])) { - if (checkSS(i, ip) || checkSS(jp, j)) - continue; - temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; /* Energy of internal loop closed by (i,j) and (ip,jp) + the energy of structure closed by (ip, jp)*/ - if (VBIij > temp) { - VBIij = temp; - ifinal = ip; - jfinal = jp; - } - } - } - - for (ip = i + 2; ip <= i + MAXLOOP + 1; ip++) { - thres1 = MAX((j - 1) + (ip - i - 1) - MAXLOOP, ip + 4); - for (jp = thres1; jp <= j - 1; jp++) { - if (jp-ip >= contact_dist) continue; - if (chPair(RNA[ip], RNA[jp])) { - if (checkSS(i, ip) || checkSS(jp, j)) - continue; - temp = eL(i, j, ip, jp) + V[indx[ip] + jp]; - if (VBIij > temp) { - VBIij = temp; - ifinal = ip; - jfinal = jp; - } - } - } - } - - if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0 - && constraints[j] != i) || constraints[i] == -1 || constraints[j] - == -1) - VBIij = INFINITY_; - - VBI[i][j] = VBIij; - /* VBI ends */ - - /* VM and WM starts */ - aupen = auPen(rnai, rnaj); - - /* Here we are doing the calculation of VM and WM at point (i,j) concurrently. The following for loop calculates the values of VMij, VMidj, VMijd, VMidjd with the value of WMijp. The value of WMijp is needed for calculating the value of WM at (i,j). However, it should be noted that the final value of WM[i][j] requires value of V at (i,j) which itself require VM(i,j), and will be calculated in the end. */ - - /* There are four possibilities for the multiloop closing base pair for the inclusion of dangling energies. - * 1) Including the dangling energy of i+1 base and also for base j-1 with the base pair (i,j) closing the multiloop - VMidjd - * 2) Including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j) - VMidj - * 3) NOT including the danlging energy of i+1 base and including the dangling energy of base j-1 with the closing base pair (i,j) - VMijd - * 4) NOT including the danlging energy of i+1 base and NOT including the dangling energy of base j-1 with the closing base pair (i,j)-VMij - * */ - - VMij = INFINITY_; - VMijd = INFINITY_; - VMidj = INFINITY_; - VMidjd = INFINITY_; - - /* Manoj starts */ - /* Merged calculations of WM(i,j) and VM(i,j)*/ - WMijp = WM[i][i + 4] + WM(i+5,j); - a1 = WM[i][i + 5] + WM(i+6,j); - if (a1 <= WMijp) - WMijp = a1; - - for (h = i + 6; h <= j - 5; h++) { - - a1 = WM[i][h]; - WMip1hm1 = WM[i + 1][h - 1]; - WMip2hm1 = WM[i + 2][h - 1]; -#if 0 - WMhjm1 = WM[h][j-1]; - WMhjm2 = WM[h][j-2]; - WMhp1j = WM[h+1][j]; -#else - WMhjm1 = WM(h,j-1); - WMhjm2 = WM(h,j-2); - WMhp1j = WM(h+1,j); -#endif - - /* WM starts */ - a1 += WMhp1j; - if (a1 <= WMijp) - WMijp = a1; - /* WM ends */ - - /* Calculation of the four options for VM*/ - A_temp = WMip1hm1 + WMhjm1; - if ((A_temp <= VMij)) - VMij = A_temp; - - A_temp = WMip2hm1 + WMhjm1; - if (A_temp <= VMidj && constraints[i + 1] <= 0) - VMidj = A_temp; - - A_temp = WMip1hm1 + WMhjm2; - if (A_temp <= VMijd && constraints[j - 1] <= 0) - VMijd = A_temp; - - A_temp = WMip2hm1 + WMhjm2; - if (A_temp <= VMidjd && constraints[i + 1] <= 0 && constraints[j - 1] - <= 0) - VMidjd = A_temp; - - // if(i==28 && j==42) - // printf("(%d,%d,%d), VMij: %d, VMidj: %d, VMijd: %d, VMidjd: %d\n", i,h,j, VMij, VMijd, VMidj, VMidjd); - - } - -#if 0 - VMidj += dangle[rnai][rnaj][RNA[i+1]][0]; - VMijd += dangle[rnai][rnaj][RNA[j-1]][1]; - VMidjd += dangle[rnai][rnaj][RNA[i+1]][0] + dangle[rnai][rnaj][RNA[j-1]][1]; -#else - tmp1 = dangle[rnai][rnaj][RNA[i + 1]][0]; - tmp2 = dangle[rnai][rnaj][RNA[j - 1]][1]; - - VMidj += tmp1; - VMidjd += tmp1; - VMijd += tmp2; - VMidjd += tmp2; -#endif - - //if(i==28 && j==42) - // printf("after for: (%d,%d,%d), VMij: %d, VMidj: %d, VMijd: %d, VMidjd: %d\n", i,h,j, VMij, VMijd, VMidj, VMidjd); - - /* Manoj ends */ - VMij = MIN(MIN(VMij, VMidj), MIN(VMijd, VMidjd)); - VMij = VMij + b + a; - VMij += aupen; - - if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0 - && constraints[j] != i) || constraints[i] == -1 || constraints[j] - == -1) - VMij = INFINITY_; - - VM[i][j] = VMij; - /* VM ends */ - - /* V starts */ - es = eS(i, j); /* Energy of stack closed with (i,j) and (i+1,j-1)*/ - if (es == 0) { /* Amrita: I don't know, if this statement is necessary. NOT DONE BY ME. */ - es = INFINITY_; - } else - es += V[indx[i + 1] + j - 1]; - - int Vij; - Vij = MIN(MIN(eH(i, j), es), MIN(VBI[i][j], VMij)); - - if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0 - && constraints[j] != i) || constraints[i] == -1 || constraints[j] - == -1) - Vij = INFINITY_; - - //printf("%d, V(%d,%d): eh: %d, es: %d, vbi: %d, vm: %d, v: %d\n", j-i, i, j, eH(i,j), es, VBI[i][j], VMij, Vij); - - V[indx[i] + j] = Vij; - - if (NOISOLATE == TRUE && Vij < INFINITY_) { - //Check if i+1,j-1 have paired - if (V[indx[i + 1] + j - 1] > INFINITY_ - SMALLINFTY_) { - //If not then check for i-1, j+1 - - //Isolated base pairs look ahead - int eHL = eH(i - 1, j + 1); - int eSL = eS(i - 1, j + 1) + V[indx[i] + j]; - if (i - 1 == 0) { - eSL = 0; - eHL = 0; - } - int Vijl = (eHL < eSL) ? eHL : eSL; - //printf("(%d,%d): Hairpin: %d, Stack: %d, Lookahead: %d\n", i, j, eHL, eSL, Vijl); - - if (Vijl > INFINITY_ - SMALLINFTY_) - //isolated base pair found.. setting energy to infinity - V[indx[i] + j] = Vij = INFINITY_; - } - } - -#if DEBUG - if (indx[i]+j > (LENGTH-1)*(LENGTH)/2) - fprintf(stderr,"ERROR: in calcVBIVMVWM: i: %5d j: %5d\n",i,j); -#endif - - /* V ends */ - - /* WM starts */ - /* No dangling base on any of the side */ - WMij = V[indx[i] + j] + aupen + b; - /* Dangling base i on 3' end of the base pair (i+1,j) */ - if (constraints[i] <= 0) - WMidj = V[indx[i + 1] + j] + dangle[rnaj][RNA[i + 1]][rnai][1] + auPen( - RNA[i + 1], rnaj) + b + c; - /* Dangling base j on 5' end of the base pair (i,j-1)*/ - if (constraints[j] <= 0) - WMijd = V[indx[i] + j - 1] + dangle[RNA[j - 1]][rnai][rnaj][0] + auPen( - rnai, RNA[j - 1]) + b + c; - /* Dangling base i on the 3' end and base j on the 5' end of the base pair (i+1,j-1)*/ - if (constraints[i] <= 0 && constraints[j] <= 0) - WMidjd = V[indx[i + 1] + j - 1] - + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1] - + dangle[RNA[j - 1]][RNA[i + 1]][rnaj][0] + auPen(RNA[i + 1], - RNA[j - 1]) + b + 2* c ; - - // if(i==36 && j==50) - // printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d\n", i, j, WMij, WMidj, WMijd, WMidjd); - - WMij = MIN(MIN(WMij, WMidj), MIN(WMijd, WMidjd)); - /* Term WM[i+1][j] takes care of the option when base i is neither pairing up nor playing the role in the dangling energy calculation and we have to add penalty 'c' for base i to remain single. - * Term WM[i][j-1] takes care of the option when base j is neither pairing up nor playing the role in the dangling energy calculations and add penalty 'c' for base j to remain single. - * */ - - int WMsip1j = INFINITY_; - int WMsijm1 = INFINITY_; - - if (constraints[i] <= 0) - WMsip1j = WM[i + 1][j]; - - if (constraints[j] <= 0) - WMsijm1 = WM[i][j - 1]; - - // if(i==36 && j==50) - // printf("(%d,%d), WMij: %d, WMsip1j: %d, WMsijm1: %d\n", i, j, WMij, WMsip1j, WMsijm1); - - - WMij = MIN(MIN(WMsip1j + c, WMsijm1 + c), WMij); - - // if(i==35 && j==50) - // printf("(%d,%d), WMij: %d, WMidj: %d, WMijd: %d, WMidjd: %d\n", i, j, WMij, WMidj, WMijd, WMidjd); - - //printf("%d, (%d,%d), WM: %d\n", j-i, i, j, WMij); - - WM[i][j] = MIN(WMijp, WMij); - WM(i,j) = WM[i][j]; /* extra instruction */ - /* WM ends */ - - return; -} - -//problems in this function.. i think this should fix it.. -/* Function to calculate the value of W[j]. */ -void calcW(int j) { - - int i; - int Wj, Widjd /*Dangling base on both sides*/, - Wijd/* Dangling base on jth side.*/, - Widj/* Dangling base on ith side */, - Wij/* No dangle base on any of the sides */, Wim1 /* Value of W at (i-1). Set to zero if positive*/; - int rnai, rnaj; - int must_branch = 0, besti = 0; - - Wj = INFINITY_; - - rnaj = RNA[j]; - - for (i = 1; i < j - 3; i++) { + } + fclose(file); + + file = fopen("Eh.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + int eh = INFINITY_; + if (PP[ii][jj]) eh = eH(ii,jj); + fprintf(file, "%d %d %d\n",ii,jj,eh>=INFINITY_?INFINITY_:eh); + } + } + fclose(file); + + file = fopen("Es.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + int es = INFINITY_; + if (PP[ii][jj] && PP[ii+1][jj-1]) es = eS(ii,jj); + fprintf(file, "%d %d %d\n",ii,jj,es>=INFINITY_?INFINITY_:es); + } + } + fclose(file); - Wij = Widjd = Wijd = Widj = INFINITY_; + file = fopen("BP.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,PP[ii][jj]); + } + } + fclose(file); - // printf("i: %d, j: %d\n", i, j); + file = fopen("VM.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,VM(ii,jj)); + } + } + fclose(file); -# if 0 - Wim1=W[i-1]; -#endif -#if 1 - Wim1 = MIN(0, W[i - 1]); /* If W[i-1] >=0, this means that there is a branch contained in the sequence from 1 to i-1. Otherwise W[i-1] will be INFINITY. Here Wim1 is defined in this manner, to make the energy of unfolded sequence as INFINITY. */ + file = fopen("WM.txt", "w"); + for (ii = 1; ii <= len; ++ii) { + for (jj = len; jj > ii; --jj) { + fprintf(file, "%d %d %d\n",ii,jj,WM(ii,jj)); + } + } + fclose(file); #endif - //Wim1 = W[i - 1]; - - rnai = RNA[i]; - - /* SH: Calculate the energy with no dangle bases. */ - Wij = V[indx[i] + j] + auPen(rnai, rnaj) + Wim1; - /* Dangle on both sides of the base pair (i+1,j-1). Add the corresponding energy. */ - if (constraints[i] <= 0 && constraints[j] <= 0) - Widjd = V[indx[i + 1] + j - 1] + auPen(RNA[i + 1], RNA[j - 1]) - + dangle[RNA[j - 1]][RNA[i + 1]][rnai][1] + dangle[RNA[j - - 1]][RNA[i + 1]][rnaj][0] + Wim1; - /* Single base j dangling on the 5' end of base pair (i,j-1) */ - if (constraints[j] <= 0) - Wijd = V[indx[i] + j - 1] + auPen(rnai, RNA[j - 1]) + dangle[RNA[j - - 1]][rnai][rnaj][0] + Wim1; - /* Single base i dangling on the 3' end of base pair (i+1,j) */ - if (constraints[i] <= 0) - Widj = V[indx[i + 1] + j] + auPen(RNA[i + 1], rnaj) - + dangle[rnaj][RNA[i + 1]][rnai][1] + Wim1; - - int tmpWj = Wj; - Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); /* Take the minimum */ - if (tmpWj != Wj) { - must_branch = 0; - besti = i; - } - - // if(i==46 && j==395){ - // printf("V(%d, %d): %d, WM: %d\n", 46, j, V[indx[46]+j], WM[46][j]); - // printf("Wij: %d, Widjd: %d, Wijd: %d, Widj: %d\n\n", Wij, Widjd, Wijd, Widj); - //} - - if (Wj < INFINITY_) { - if (Wj == Wij) { - if (constraints[i] == j) { - must_branch = 1; - } - } else if (Wj == Widjd) { - if (constraints[i + 1] == j - 1) { - must_branch = 1; - } - } else if (Wj == Wijd) { - if (constraints[i] == j - 1) { - must_branch = 1; - } - } else { - if (constraints[i + 1] == j) { - must_branch = 1; - } - } - } - - } - - //printf("W%dcal: %d, must_branch: %d, best_i: %d", j, Wj, must_branch, besti); - - /* If jth base is not contributing in the energy calculation of W[j] */ - if (!must_branch) { - if (Wj > W[j - 1]) - Wj = W[j - 1]; - } - - W[j] = Wj; - - //printf(",W%dset: %d\n", j, W[j]); - - // if(j==11 || j==35 || j==36) - // printf("\n*****\nMust branch: %d, W%d: %d\n*****\n", must_branch, j, W[j]); - return; -} - -/* For details on calculating energy of different types of Internal loops, please look at the chapter 3 of MS thesis of Mirela Stefania Andronescu. - * http://www.cs.ubc.ca/grads/resources/thesis/Nov03/Mirela_Andronescu.pdf - * */ -/* Calculates the energy of internal loop with (i,j) as closing base pair and (ip,jp) as enclosed base pair */ -int eL(int i, int j, int ip, int jp) { - - int energy; - int size1, size2, size; - int loginc; /* SH: Originally unassiged, but needs to be set to 0 so it doesn't throw off later calculations. */ - int lopsided; /* define the asymmetry of an interior loop */ - - energy = INFINITY_; - loginc = 0; - - /*SH: These calculations used to incorrectly be within the bulge loop code, moved out here. */ - size1 = ip - i - 1; - size2 = j - jp - 1; - size = size1 + size2; - - if (size1 == 0 || size2 == 0) { - if (size > 30) { - /* AM: Does not depend upon i and j and ip and jp - Stacking Energies */ - loginc = (int) floor(prelog * log((double) size / 30.0)); - energy = bulge[30] + eparam[2] + loginc + auPen(RNA[i], RNA[j]) - + auPen(RNA[ip], RNA[jp]); - } else if (size <= 30 && size != 1) { - /* Does not depend upon i and j and ip and jp - Stacking Energies */ - energy = bulge[size] + eparam[2]; - energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]); - } else if (size == 1) { - energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])] - + bulge[size] + eparam[2]; /* mans */ - } - } else { - /* Internal loop */ - lopsided = abs(size1 - size2); - - if (size > 30) { - loginc = (int) floor(prelog * log((double) size / 30.0)); - - /* Please check what should be the difference in the following two options. Is it correct?*/ - if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/ - - energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp - + 1], RNA[ip - 1])] + inter[30] + loginc + eparam[3] - + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, - size2))])); - } else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/ - energy - = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] - + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, - BASE_A)] + inter[30] + loginc - + eparam[3] + MIN(maxpen, (lopsided - * poppen[MIN(2, MIN(size1, size2))])); - } - } - /* if size is not > 30, we have a looooot of cases... */ - else if (size1 == 2 && size2 == 2) { - /* 2x2 internal loop */ - energy - = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i - + 2]][RNA[j - 1]][RNA[j - 2]]; - } else if (size1 == 1 && size2 == 2) { - energy - = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; - } else if (size1 == 2 && size2 == 1) { - /* 1x2 internal loop */ - energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i - + 1]][RNA[j]][RNA[i]]; - } else if (size == 2) { - /* 1*1 internal loops */ - energy - = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]]; - } else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) */ - energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] - + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)] - + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided - * poppen[MIN(2, MIN(size1, size2))])); - } else { /* General Internal loops */ - energy - = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], - RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], - RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size] - + loginc + eparam[3] /* AM: I don't understand this eparam value, I think they do not play any role currently. Please look in loader.cc file, for what value have been assinged to various elements of eparam array */ - + MIN(maxpen, - (lopsided * poppen[MIN(2, MIN(size1, size2))])); /* */ - } - } - - return energy; -} - -/* For details on calculating energy of different types of hairpin loops, please look at the chapter 3 of MS thesis of Mirela Stefania Andronescu. - * http://www.cs.ubc.ca/grads/resources/thesis/Nov03/Mirela_Andronescu.pdf - * */ -/* SH: Function used to calculate energy of a hairpin loop between i & j. */ -/* inline */ -int eH(int i, int j) { - /* Hairpin loop for all the bases between i and j */ - /* size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */ - int size; - int loginc; - int energy = INFINITY_; - int key, index, count, tlink, kmult; - - size = j - i - 1; /* size is the number of bases in the loop, when the closing pair is excluded */ - - //checking if single stranded region is allowed with given constraints - if (checkSS(i, j) || (constraints[i] > 0 && constraints[i] != j) - || (constraints[j] > 0 && constraints[j] != i)) - return energy; - - /* look in hairpin, and be careful that there is only 30 values */ - - if (size > 30) { - loginc = (int) ((prelog) * log(((double) size) / 30.0)); - energy = hairpin[30] + loginc + tstkh[fourBaseIndex(RNA[i], RNA[j], - RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/ - } - - else if (size <= 30 && size > 4) { - energy = hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j], - RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/ - } - - else if (size == 4) { - /* tetraloop */ - key = 0; - tlink = 0; - for (index = 0; index < 6; ++index) { - switch (RNA[i + index]) { - case BASE_A: - kmult = 1; - break; - case BASE_C: - kmult = 2; - break; - case BASE_G: - kmult = 3; - break; - case BASE_U: - kmult = 4; - break; - default: - kmult = 0; - fprintf(stderr, "ERROR: in tetraloop calculation\n"); - } - key += kmult * (int) pow(10.0, 5 - index); - } - /* if the sequence is in tloop, we use this value */ - for (count = 1; count < numoftloops && tlink == 0; ++count) { - if (key == tloop[count][0]) { - tlink = tloop[count][1]; - } - } - energy = tlink + hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j], - RNA[i + 1], RNA[j - 1])] + eparam[4]; - } - - else if (size == 3) { - /* triloop... For the moment, the file triloop.dat is empty */ - /* else, should have a treatment like the one if size==4 */ - energy = hairpin[size]; - /* AM: Don't include stacking energy terms for triloopls */ - /* + tstkh[RNA[i]][RNA[j]][RNA[i+1]][RNA[j-1]] */ - /* + eparam[4]; */ - /* Must be another penalty for terminal AU... Not sure of this */ - energy += auPen(RNA[i], RNA[j]); - } - - else if (size < 3 && size != 0) { - /* no terminal mismatch */ - energy = hairpin[size] + eparam[4]; - if ((RNA[i] == BASE_A && RNA[j] == BASE_U) || (RNA[i] == BASE_U - && RNA[j] == BASE_A)) { - energy += 6; /* Seems to be a penalty for terminal AU. *//* Hairpin Loops of size 3 are not allowed, the term hairpin[size] will result in a very large value. */ - } - } else if (size == 0) - return INFINITY_; - - /* GGG Bonus => GU closure preceded by GG */ - /* i-2 = i-1 = i = G, and j = U; i < j */ - if (i > 2) { - if (RNA[i - 2] == BASE_G && RNA[i - 1] == BASE_G && RNA[i] == BASE_G - && RNA[j] == BASE_U) { - energy += gubonus; - /* printf ("\n GGG bonus for i %d j %d ", i, j); */ - } - } - - /* Poly-C loop => How many C are needed for being a poly-C loop */ - tlink = 1; - for (index = 1; (index <= size) && (tlink == 1); ++index) { - if (RNA[i + index] != BASE_C) - tlink = 0; - } - if (tlink == 1) { - if (size == 3) { - energy += c3; - } else { - energy += cint + size * cslope; - } - } - - return energy; -} - -/* SH: Function used to calculate energy of stacked pairs (i.j) & (i+1.j-1). */ -/* inline */ -int eS(int i, int j) { - int energy; - - if ((constraints[i] > 0 && constraints[i] != j) || (constraints[j] > 0 - && constraints[j] != i)) - return INFINITY_; - - //if (j - i <= 3) - // return INFINITY_; - - /* not sure about eparam[1], come from MFold.. = 0 */ - energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] - + eparam[1]; - - return energy; + return W[len]; } diff --git a/gtfold-mfe/src/boltzmann_main.cc b/gtfold-mfe/src/boltzmann_main.cc new file mode 100644 index 0000000..b423c0e --- /dev/null +++ b/gtfold-mfe/src/boltzmann_main.cc @@ -0,0 +1,225 @@ +#include +#include +#include +#include +#include + +#include "global.h" +#include "loader.h" +#include "algorithms-partition.h" +#include "boltzmann_main.h" +#include "partition-func.h" +#include "mfe_main.h" +#include "stochastic-sampling.h" +#include "algorithms.h" +#include "traceback.h" + +using namespace std; + +static bool CALC_PART_FUNC = false; +static bool PF_COUNT_MODE = false; +static bool BPP_ENABLED = false; +static bool PARAM_DIR = false; +static bool RND_SAMPLE = false; +static bool CALC_PF_DO = false; +static bool CALC_PF_DS = false; + +static string seqfile = ""; +static string outputPrefix = ""; +static string outputDir = ""; +static string outputFile = ""; +static string paramDir; // default value +static string bppOutFile = ""; +static int num_rnd = 0; + +static void help() { + printf("Usage: gtboltzmann [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + + printf(" --partition Calculate the partition function (default is using sfold reccurences).\n"); + printf(" --partition -dS Calculate the partition function using sfold reccurences.\n"); + printf(" --partition -d0 Calculate the partition function using -d0 reccurences.\n"); + printf(" --partition -d2 Calculate the partition function using -d2 reccurences (Under implementation).\n"); + + printf(" --sample INT Sample number of structures equal to INT\n"); + printf(" --pfcount Calculate the structure count using partition function and zero energy value.\n"); + printf(" --bpp Calculate base pair probabilities.\n"); + printf("\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + exit(-1); +} + +static void parse_options(int argc, char** argv) { + int i; + + for(i=1; i 0) { + outputPrefix = outputPrefix.substr(pos+1); + } + + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; +} + + +int boltzmann_main(int argc, char** argv) { + std::string seq; + + parse_options(argc, argv); + + if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { + printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); + exit(-1); + } + + init_fold(seq.c_str()); + + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, 0, 0, 0); + + if (CALC_PART_FUNC == true && CALC_PF_DS == true) { + printf("\nComputing partition function in -dS mode ...\n"); + calculate_partition(seq.length(),0); + free_partition(); + } + else if (CALC_PART_FUNC == true && CALC_PF_DO == true) { + printf("\nCalculating partition function in -d0 mode ...\n"); + double ** Q, **QM, **QB, **P; + Q = mallocTwoD(seq.length() + 1, seq.length() + 1); + QM = mallocTwoD(seq.length() + 1, seq.length() + 1); + QB = mallocTwoD(seq.length() + 1, seq.length() + 1); + P = mallocTwoD(seq.length() + 1, seq.length() + 1); + + + fill_partition_fn_arrays(seq.length(), Q, QB, QM); + freeTwoD(Q, seq.length() + 1, seq.length() + 1); + freeTwoD(QM, seq.length() + 1, seq.length() + 1); + freeTwoD(QB, seq.length() + 1, seq.length() + 1); + freeTwoD(P, seq.length() + 1, seq.length() + 1); + } + else if (CALC_PART_FUNC == true) { + printf("\nComputing partition function...\n"); + int pf_count_mode = 0; + if(PF_COUNT_MODE) pf_count_mode=1; + + calculate_partition(seq.length(),pf_count_mode); + free_partition(); + } else if (RND_SAMPLE == true) { + printf("\nComputing partition function...\n"); + int pf_count_mode = 0; + if(PF_COUNT_MODE) pf_count_mode=1; + double U = calculate_partition(seq.length(),pf_count_mode); + + batch_sample(num_rnd, seq.length(), U); + + free_partition(); + } else if(BPP_ENABLED) { + printf("\n"); + printf("Calculating partition function\n"); + double ** Q, **QM, **QB, **P; + Q = mallocTwoD(seq.length() + 1, seq.length() + 1); + QM = mallocTwoD(seq.length() + 1, seq.length() + 1); + QB = mallocTwoD(seq.length() + 1, seq.length() + 1); + P = mallocTwoD(seq.length() + 1, seq.length() + 1); + + + fill_partition_fn_arrays(seq.length(), Q, QB, QM); + fillBasePairProbabilities(seq.length(), Q, QB, QM, P); + printBasePairProbabilities(seq.length(), structure, P, bppOutFile.c_str()); + printf("Saved BPP output in %s\n",bppOutFile.c_str()); + + freeTwoD(Q, seq.length() + 1, seq.length() + 1); + freeTwoD(QM, seq.length() + 1, seq.length() + 1); + freeTwoD(QB, seq.length() + 1, seq.length() + 1); + freeTwoD(P, seq.length() + 1, seq.length() + 1); + } else { + printf("No valid option specified !\n\n"); + help(); + } + + free_fold(seq.length()); + return EXIT_SUCCESS; +} diff --git a/gtfold-mfe/src/constraints.cc b/gtfold-mfe/src/constraints.cc new file mode 100644 index 0000000..b1f2a1b --- /dev/null +++ b/gtfold-mfe/src/constraints.cc @@ -0,0 +1,542 @@ +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "global.h" +#include "options.h" +#include "constraints.h" + +int* BP; +int* ind; + +typedef pair basepair_t; + +/* +ZS: Explanation to BP array. + +BP(i,j) for i!=j can have one of the following values: +0: Nothing is required about a pair i,j in constraints +1: Force pairing between i and j. This implies also that + any non-nested pairings will be prohibited and any + other pairs i and j would be involved in are also prohibited. +2: Prohibit pairing between i and j. (Nothing else is done) + +BP(i,i) can have one of the following values: +0: Nothing is known about position i at all +3: Position i is forced to be single-stranded. This implies also that + any pairs with i will be prohibited. +4: Position i is NOT single-stranded, it is forced to be in a pair. +5: Position i is prohibited from pairing with at least one nucleotide. +*/ + +int** PBP; +int** FBP; + +int nPBP; +int nFBP; + +static bool CONS_ENABLED = false; +static bool LIMIT_DISTANCE = false; +static int contactDistance = -1; + +void enable_constraints(int b) {CONS_ENABLED = b;} +void enable_limit_distance(int b) {LIMIT_DISTANCE = b;} +void set_contact_distance(int dist) {contactDistance = dist;} + +static int load_constraints(const char* constr_file, int seq_length, int verbose=0) { + + fprintf(stdout, "- Running with constraints\n"); + + std::ifstream cfcons; + cfcons.open(constr_file, std::ios::in); + if (cfcons == 0) { + fprintf(stderr, "Error opening constraint file\n\n"); + cfcons.close(); + return -1; + } + + char cons[100]; + + while (!cfcons.eof()) { + cfcons.getline(cons, 100); + if (cons[0] == 'F' || cons[0] == 'f') nFBP++; + if (cons[0] == 'P' || cons[0] == 'p') nPBP++; + } + cfcons.close(); + + //fprintf(stdout, "Number of Constraints given: %d\n\n", nFBP + nPBP); + if (nFBP + nPBP == 0) { + fprintf(stderr, "No Constraints found.\n\n"); + return -1; + } + + FBP = (int**) malloc(nFBP*sizeof(int*)); + PBP = (int**) malloc(nPBP*sizeof(int*)); + + int fit = 0, pit = 0, it = 0; + + for (it = 0; it < nFBP; it++) { + FBP[it] = (int*) malloc(2* sizeof (int)); + } + for(it=0; it < nPBP; it++) { + PBP[it] = (int*)malloc(2*sizeof(int)); + } + cfcons.open(constr_file, std::ios::in); + + while(!cfcons.eof()) { + cfcons.getline(cons,100); + char *p=strtok(cons, " "); + p = strtok(0, " "); + if(cons[0]=='F' || cons[0]=='f') { + int fit1=0; + while(p!=0) { + FBP[fit][fit1++] = atoi(p); + p = strtok(0, " "); + } + fit++; + } + if(cons[0]=='P' || cons[0]=='p') { + int pit1=0; + while(p!=0) { + PBP[pit][pit1++] = atoi(p); + p = strtok(0, " "); + } + pit++; + } + } + + map all_bases; + for(it=0; it< nFBP; it++) { + for(int k=1;k<= FBP[it][2];k++) { + basepair_t base_pair(FBP[it][0]+k-1, FBP[it][1]-k+1); + pair::iterator, bool> retVal; + retVal = all_bases.insert(pair(base_pair.first, base_pair)); + if (base_pair.first < 1 || base_pair.first > seq_length) { + fprintf(stderr, "\nBase %d from constraint (%d,%d) is out of bounds of the sequence which has length %d \n", + base_pair.first, base_pair.first, base_pair.second, seq_length); + exit(1); + } + if (base_pair.second < 1 || base_pair.second > seq_length) { + fprintf(stderr, "\nBase %d from constraint (%d,%d) is out of bounds of the sequence which has length %d \n", + base_pair.second, base_pair.first, base_pair.second, seq_length); + exit(1); + } + if (base_pair.first >= base_pair.second - TURN) { + fprintf(stderr, "\nDistance between bases of base pair (%d,%d) is too small\n", + base_pair.first, base_pair.second); + exit(1); + } + if (retVal.second == false) { + fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n", + base_pair.first, base_pair.first, base_pair.second); + exit(1); + } + retVal = all_bases.insert(pair(base_pair.second, base_pair) ); + if (retVal.second == false) { + fprintf(stderr, "\nDuplicate base %d encountered in Constraints. Base Pair %d,%d\n", + base_pair.first, base_pair.first, base_pair.second); + exit(1); + } + } + } + + vector verify_stack; + for (map::iterator it = all_bases.begin(); it != all_bases.end(); ++it) { + + pair map_element = (*it); + int base = map_element.first; + basepair_t base_pair = map_element.second; + if (base_pair.first == base) { + verify_stack.push_back(base_pair); + } else { + basepair_t last_base_pair = verify_stack.back(); + if (last_base_pair.second == base) { + verify_stack.pop_back(); + } + else { + fprintf(stderr, "\nConstraints create pseudoknots, exiting !!!\n"); + exit(1); + } + } + } + + return 0; +} + +int init_constraints(const char* constr_file,int length) { + enable_constraints(true); + load_constraints(constr_file, length); + + + int i,j,it,k; + ind = (int*) malloc((length+1) * sizeof(int)); + if (ind == NULL) { + perror("Cannot allocate variable 'ind'"); + exit(-1); + } + for(i = 1; i<=length; i++){ + ind[i] = (i*(i-1)) >> 1; //n(n-1)/2 + } + + + BP = (int*) malloc((((length+1)*(length))/2+1)*sizeof(int)); + if (BP == NULL) { + perror("Cannot allocate variable 'constraints'"); + exit(-1); + } + + int LLL = length*(length+1)/2 + 1; + + + //ZS: initialize all basepairing constraints to 0 (default is nothing known) + for(i = 0; i PBP[it][1] && PBP[it][1]!=0){ + temp = PBP[it][0]; + PBP[it][0] = PBP[it][1]; + PBP[it][1] = temp; + } + } + + for(it = 0; it < nPBP; it++){ + if(PBP[it][2] < 1){ + printf("Invalid entry (P: %d %d %d)\n", PBP[it][0], PBP[it][1], PBP[it][2]); + continue; + } + + for(k = 1; k <= PBP[it][2]; k++){ + + if(PBP[it][1] == 0){ + //force single-stranded + BP(PBP[it][0]+k-1, PBP[it][0]+k-1) = 3; + //prohibit all pairs with that base + for(i = 1; i<=length; i++){ + if(i FBP[it][1]){ + temp = FBP[it][0]; + FBP[it][0] = FBP[it][1]; + FBP[it][1] = temp; + } + } + for(it = 0; it +#include +#include + +#include "energy.h" +#include "utils.h" +#include "global.h" +#include "constants.h" +#include "shapereader.h" + +int *V; +int *W; +int *VBI; +int *VM; +int **WM; +int **WMPrime; +int *indx; +int **PP; + +int alloc_flag = 0; +const float RT = ((0.00198721 * 310.15)*100); //* 100.00); +const float RT_ = (0.00198721 * 310.15); + +void create_tables(int len) { + V = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int)); + if (V == NULL) { + perror("Cannot allocate variable 'V'"); + exit(-1); + } + + int i; + WM = (int **) malloc((len+1)* sizeof(int *)); + if (WM == NULL) { + perror("Cannot allocate variable 'WM'"); + exit(-1); + } + for (i = 0; i <= len; i++) { + WM[i] = (int *)malloc((len+1)* sizeof(int)); + if (WM[i] == NULL) { + perror("Cannot allocate variable 'WM[i]'"); + exit(-1); + } + } + + PP = (int **) malloc((len+1)* sizeof(int *)); + if (PP == NULL) { + perror("Cannot allocate variable 'WM'"); + exit(-1); + } + for (i = 0; i <= len; i++) { + PP[i] = (int *)malloc((len+1)* sizeof(int)); + if (PP[i] == NULL) { + perror("Cannot allocate variable 'WM[i]'"); + exit(-1); + } + } + + WMPrime = (int **) malloc((len+1)* sizeof(int *)); + if (WMPrime == NULL) { + perror("Cannot allocate variable 'WM'"); + exit(-1); + } + for (i = 0; i <= len; i++) { + WMPrime[i] = (int *)malloc((len+1)* sizeof(int)); + if (WMPrime[i] == NULL) { + perror("Cannot allocate variable 'WM[i]'"); + exit(-1); + } + } + + VM = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int)); + if (VM == NULL) { + perror("Cannot allocate variable 'V'"); + exit(-1); + } + + VBI = (int *) malloc(((len+1)*len/2 + 1) * sizeof(int)); + if (VBI == NULL) { + perror("Cannot allocate variable 'V'"); + exit(-1); + } + + W = (int *) malloc((len+1) * sizeof(int)); + if (W == NULL) { + perror("Cannot allocate variable 'W'"); + exit(-1); + } + + indx = (int*) malloc((len+1) * sizeof(int)); + if (indx == NULL) { + perror("Cannot allocate variable 'indx'"); + exit(-1); + } + + alloc_flag = 1; + + init_tables(len); +} + + +void init_tables(int len) { + int i, j, LLL; + + for (i = 0; i <= len; i++) { + W[i] = INFINITY_; + for (j = 0; j <= len; j++) { + WM[i][j] = INFINITY_; + WMPrime[i][j] = INFINITY_; + PP[i][j] = 0; + } + } + + LLL = (len)*(len+1)/2 + 1; + for (i = 0; i < LLL; i++) { + V[i] = INFINITY_; + VM[i] = INFINITY_; + VBI[i] = INFINITY_; + } + + for (i = 1; i <= (unsigned) len; i++) + indx[i] = (i*(i-1)) >> 1; /* n(n-1)/2 */ + + return; +} + +void free_tables(int len) { + if (alloc_flag == 1) { + free(indx); + + int i; + for (i = 0; i <= len; i++) free(WM[i]); + free(WM); + + for (i = 0; i <= len; i++) free(WMPrime[i]); + free(WMPrime); + + free(VM); + free(VBI); + free(V); + free(W); + } +} + + +inline int Ed3(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][1];} +inline int Ed5(int i, int j, int k) { return dangle[RNA[i]][RNA[j]][RNA[k]][0]; } +inline int auPenalty(int i, int j) { return auPen(RNA[i], RNA[j]);} + +inline int eL1(int i, int j, int ip, int jp) { + int energy; + int size1, size2, size; + int loginc; /* SH: Originally unassiged, but needs to be set to 0 so it doesn't throw off later calculations. */ + int lopsided; /* define the asymmetry of an interior loop */ + + energy = INFINITY_; + loginc = 0; + + /*SH: These calculations used to incorrectly be within the bulge loop code, moved out here. */ + size1 = ip - i - 1; + size2 = j - jp - 1; + size = size1 + size2; + + if (size1 == 0 || size2 == 0) { + if (size > 30) { + /* AM: Does not depend upon i and j and ip and jp - Stacking Energies */ + loginc = (int) floor(prelog * log((double) size / 30.0)); + energy = bulge[30] + eparam[2] + loginc + auPen(RNA[i], RNA[j]) + + auPen(RNA[ip], RNA[jp]); + } else if (size <= 30 && size != 1) { + /* Does not depend upon i and j and ip and jp - Stacking Energies */ + energy = bulge[size] + eparam[2]; + energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]); + } else if (size == 1) { + energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])] + + bulge[size] + eparam[2] + + + getShapeEnergy(i) + getShapeEnergy(j) + getShapeEnergy(ip) + getShapeEnergy(jp); + } + } else { + /* Internal loop */ + lopsided = abs(size1 - size2); + + if (size > 30) { + loginc = (int) floor(prelog * log((double) size / 30.0)); + + if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/ + + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[30] + loginc + + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, + BASE_A)] + inter[30] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } + } + else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */ + energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]]; + } else if (size1 == 1 && size2 == 2) { + energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; + } else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */ + energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]]; + } else if (size == 2) { /* 1*1 internal loops */ + energy = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]]; + } else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) { + return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] + + tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]]; + } + else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)] + + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } else { /* General Internal loops */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size] + + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + + } + } + + return energy; +} + +inline int eL(int i, int j, int ip, int jp) { + int energy; + int size1, size2, size; + int loginc; /* SH: Originally unassiged, but needs to be set to 0 so it doesn't throw off later calculations. */ + int lopsided; /* define the asymmetry of an interior loop */ + + energy = INFINITY_; + loginc = 0; + + /*SH: These calculations used to incorrectly be within the bulge loop code, moved out here. */ + size1 = ip - i - 1; + size2 = j - jp - 1; + size = size1 + size2; + + if (size1 == 0 || size2 == 0) { + if (size > 30) { + /* AM: Does not depend upon i and j and ip and jp - Stacking Energies */ + loginc = (int) floor(prelog * log((double) size / 30.0)); + energy = bulge[30] + eparam[2] + loginc + auPen(RNA[i], RNA[j]) + + auPen(RNA[ip], RNA[jp]); + } else if (size <= 30 && size != 1) { + /* Does not depend upon i and j and ip and jp - Stacking Energies */ + energy = bulge[size] + eparam[2]; + energy += auPen(RNA[i], RNA[j]) + auPen(RNA[ip], RNA[jp]); + } else if (size == 1) { + energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[ip], RNA[jp])] + + bulge[size] + eparam[2] + + + getShapeEnergy(i) + getShapeEnergy(j) + getShapeEnergy(ip) + getShapeEnergy(jp); + } + } else { + /* Internal loop */ + lopsided = abs(size1 - size2); + + if (size > 30) { + loginc = (int) floor(prelog * log((double) size / 30.0)); + + if (!((size1 == 1 || size2 == 1) && gail)) { /* normal internal loop with size > 30*/ + + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[30] + loginc + + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } else { /* if size is more than 30 and it is a grossely asymmetric internal loop and gail is not zero*/ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, + BASE_A)] + inter[30] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } + } + else if (size1 == 2 && size2 == 2) { /* 2x2 internal loop */ + energy = iloop22[RNA[i]][RNA[ip]][RNA[j]][RNA[jp]][RNA[i + 1]][RNA[i + 2]][RNA[j - 1]][RNA[j - 2]]; + } else if (size1 == 1 && size2 == 2) { + energy = iloop21[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]][RNA[j - 2]][RNA[ip]][RNA[jp]]; + } else if (size1 == 2 && size2 == 1) { /* 1x2 internal loop */ + energy = iloop21[RNA[jp]][RNA[ip]][RNA[j - 1]][RNA[i + 2]][RNA[i + 1]][RNA[j]][RNA[i]]; + } else if (size == 2) { /* 1*1 internal loops */ + energy = iloop11[RNA[i]][RNA[i + 1]][RNA[ip]][RNA[j]][RNA[j - 1]][RNA[jp]]; + } + //else if ((size1 == 2 && size2 == 3) || (size1 == 3 && size2 == 2)) { + // return tstacki23[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]] + + // tstacki23[RNA[jp]][RNA[ip]][RNA[jp + 1]][RNA[ip - 1]]; + //} + else if ((size1 == 1 || size2 == 1) && gail) { /* gail = (Grossly Asymmetric Interior Loop Rule) (on/off <-> 1/0) */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], BASE_A, BASE_A)] + tstki[fourBaseIndex(RNA[jp], RNA[ip], BASE_A, BASE_A)] + + inter[size] + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + } else { /* General Internal loops */ + energy = tstki[fourBaseIndex(RNA[i], RNA[j], RNA[i + 1], RNA[j - 1])] + tstki[fourBaseIndex(RNA[jp], RNA[ip], RNA[jp + 1], RNA[ip - 1])] + inter[size] + + loginc + eparam[3] + MIN(maxpen, (lopsided * poppen[MIN(2, MIN(size1, size2))])); + + } + } + + return energy; +} + +inline int eH(int i, int j) { + /* Hairpin loop for all the bases between i and j */ + /* size for size of the loop, energy is the result, loginc is for the extrapolation for loops bigger than 30 */ + int size; + int loginc; + int energy = INFINITY_; + int key, index, count, tlink, kmult; + + size = j - i - 1; /* size is the number of bases in the loop, when the closing pair is excluded */ + + /* look in hairpin, and be careful that there is only 30 values */ + + if (size > 30) { + loginc = (int) ((prelog) * log(((double) size) / 30.0)); + energy = hairpin[30] + loginc + tstkh[fourBaseIndex(RNA[i], RNA[j], + RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/ + } + + else if (size <= 30 && size > 4) { + energy = hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j], + RNA[i + 1], RNA[j - 1])] + eparam[4]; /* size penalty + terminal mismatch stacking energy*/ + } + + else if (size == 4) { + /* tetraloop */ + key = 0; + tlink = 0; + for (index = 0; index < 6; ++index) { + switch (RNA[i + index]) { + case BASE_A: + kmult = 1; + break; + case BASE_C: + kmult = 2; + break; + case BASE_G: + kmult = 3; + break; + case BASE_U: + kmult = 4; + break; + default: + kmult = 0; + fprintf(stderr, "ERROR: in tetraloop calculation\n"); + } + key += kmult * (int) pow(10.0, 5 - index); + } + /* if the sequence is in tloop, we use this value */ + for (count = 1; count < numoftloops && tlink == 0; ++count) { + if (key == tloop[count][0]) { + tlink = tloop[count][1]; + } + } + energy = tlink + hairpin[size] + tstkh[fourBaseIndex(RNA[i], RNA[j], + RNA[i + 1], RNA[j - 1])] + eparam[4]; + } + + else if (size == 3) { + /* triloop... For the moment, the file triloop.dat is empty */ + /* else, should have a treatment like the one if size==4 */ + energy = hairpin[size]; + /* AM: Don't include stacking energy terms for triloopls */ + /* + tstkh[RNA[i]][RNA[j]][RNA[i+1]][RNA[j-1]] */ + /* + eparam[4]; */ + /* Must be another penalty for terminal AU... Not sure of this */ + energy += auPen(RNA[i], RNA[j]); + } + + else if (size < 3 && size != 0) { + /* no terminal mismatch */ + energy = hairpin[size] + eparam[4]; + if ((RNA[i] == BASE_A && RNA[j] == BASE_U) || (RNA[i] == BASE_U + && RNA[j] == BASE_A)) { + energy += 6; /* Seems to be a penalty for terminal AU. *//* Hairpin Loops of size 3 are not allowed, the term hairpin[size] will result in a very large value. */ + } + } else if (size == 0) + return INFINITY_; + + /* GGG Bonus => GU closure preceded by GG */ + /* i-2 = i-1 = i = G, and j = U; i < j */ + if (i > 2) { + if (RNA[i - 2] == BASE_G && RNA[i - 1] == BASE_G && RNA[i] == BASE_G + && RNA[j] == BASE_U) { + energy += gubonus; + /* printf ("\n GGG bonus for i %d j %d ", i, j); */ + } + } + + /* Poly-C loop => How many C are needed for being a poly-C loop */ + tlink = 1; + for (index = 1; (index <= size) && (tlink == 1); ++index) { + if (RNA[i + index] != BASE_C) + tlink = 0; + } + if (tlink == 1) { + if (size == 3) { + energy += c3; + } else { + energy += cint + size * cslope; + } + } + + return energy; +} + +inline int eS(int i, int j) { + int energy; + /* not sure about eparam[1], come from MFold.. = 0 */ + energy = stack[fourBaseIndex(RNA[i], RNA[j], RNA[i+1], RNA[j-1])] + eparam[1] + + getShapeEnergy(i) + getShapeEnergy(j) + getShapeEnergy(i+1) + getShapeEnergy(j-1) ; + + return energy; +} + +inline int Estackm(int i, int j) { + return tstackm[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]]; +} + +inline int Estacke(int i, int j) { + return tstacke[RNA[i]][RNA[j]][RNA[i + 1]][RNA[j - 1]]; +} diff --git a/gtfold-mfe/src/global.cc b/gtfold-mfe/src/global.cc new file mode 100644 index 0000000..eb91d90 --- /dev/null +++ b/gtfold-mfe/src/global.cc @@ -0,0 +1,227 @@ +#include +#include +#include + +#include "utils.h" +#include "global.h" +#include "constraints.h" + +unsigned char *RNA; +int *structure; +unsigned int chPairKey; + +int g_nthreads; +int g_dangles; +int g_unamode; +int g_mismatch; +int g_verbose; +int g_prefilter_mode; +int g_prefilter1; +int g_prefilter2; + +void init_global_params(int len) { + RNA = (unsigned char *) malloc((len+1)* sizeof(unsigned char)); + if (RNA == NULL) { + perror("Cannot allocate variable 'RNA'"); + exit(-1); + } + structure = (int *) malloc((len+1) * sizeof(int)); + if (structure == NULL) { + perror("Cannot allocate variable 'structure'"); + exit(-1); + } + + init_checkPair(); +} + +void free_global_params() { + free(structure); + free(RNA); +} + +void print_sequence(int len) { + int i; + for (i = 1; i <= len; i++) { + if (RNA[i] == BASE_A) + printf("A"); + else if (RNA[i] == BASE_C) + printf("C"); + else if (RNA[i] == BASE_G) + printf("G"); + else if (RNA[i] == BASE_U) + printf("U"); + else + printf("N"); + } + printf("\n"); +} + +void print_structure(int len) { + int i = 1; + for (i = 1; i <= len; i++) + { + if (structure[i] > 0 && structure[i] > i) + printf("("); + else if (structure[i] > 0 && structure[i] < i) + printf(")"); + else + printf("."); + } + printf("\n"); +} + +int read_sequence_file(const char* filename, std::string& seq) { + seq = ""; + + ifstream fs; + fs.open(filename, ios::in); + if (!fs.good()) return FAILURE; + + string line; + while(fs.good()) { + getline(fs, line); + // exclude lines starting with FASTA comment characters + if(line[0] != ';' && line[0] != '>' && line.length() > 0) + seq += line; + } + + fs.close(); + + size_t loc; + while((loc = seq.find(" ")) != string::npos) + seq.erase(loc, 1); + + return SUCCESS; +} + +bool encodeSequence(string seq) { + unsigned int unspecifiedBaseCount=0; + unsigned int unspecifiedBases[seq.length()]; + + for(unsigned int i=1; i<=seq.length(); i++) { + RNA[i] = encode(seq[i-1]); + + // die on non-IUPAC codes + if (RNA[i]=='X') { + fprintf(stderr, "ERROR: Non-IUPAC nucleotide code at position: %d (%c)\n", i, seq[i-1]); + fprintf(stderr, "See http://www.bioinformatics.org/sms/iupac.html for valid codes.\n"); + return false; + } + + // add non-canonical IUPAC codes to the warning list + if(!isWatsonCrickBase(seq[i-1])) + unspecifiedBases[unspecifiedBaseCount++]=i; + } + + // just print a warning for non-canonical IUPAC codes + if(unspecifiedBaseCount > 0) { + printf("\nIncompletely-specified IUPAC codes have been detected at position%s: ", unspecifiedBaseCount == 1 ? "" : "s"); + + // put [0] first for nice comma separation + printf("%d (%c)", unspecifiedBases[0], seq.at(unspecifiedBases[0]-1)); + for(unsigned int i=1; i= 0 && i <=3 )&&(j >=0 && j <=3))) + return r; + if (!(chPairKey & (1 << ((i << 2) + j)))) { + chPairKey += 1 << ((i << 2) + j); + r = 1; + } + return r; +} + +int canPair(int a, int b) { + return (chPairKey & (1 << (((a)<<2) + (b)))); +} + +/* +void help() { + printf("Usage: gtfold [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + printf(" -c, --constraints FILE\n"); + printf(" Load constraints from FILE. See Constraint syntax below.\n"); + printf(" -d, --dangle INT Restricts treatment of dangling energies (INT=0,2),\n"); + printf(" see below for details.\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); + printf(" limit is given, base pairs can be over any distance.\n"); + printf(" -m --mismatch Enable terminal mismatch calculations\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming.\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -t, --threads INT Limit number of threads used to INT.\n"); + printf(" -v, --verbose Run in verbose mode (includes loop-by-loop energy decomposition\n"); + printf(" and confirmation of constraints satisfied).\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); + printf(" neighboring nucleotides such that it could be part of\n"); + printf(" a helix of length INT.\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5).\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8), subject to traceback\n"); + printf(" implementation.\n"); + + printf("\nBETA OPTIONS\n"); + printf(" --bpp Calculate base pair probabilities.\n"); + printf(" --partition Calculate the partition function.\n"); + printf(" --pf_count Calculate the structure count using partition function and zero energy value.\n"); + printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); + printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); + + printf("\nConstraint syntax:\n"); + printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); + + printf("\nDangle:\n"); + printf("\tINT=0 ignores dangling energies (mostly for debugging).\n"); + printf("\tINT=2 dangling energies are added for nucleotides on either\n"); + printf("\tside of each branch in multi-loops and external loops.\n"); + printf("\tAll other values for INT are ignored.\n"); + exit(-1); +} +*/ diff --git a/gtfold-mfe/src/loader.cc b/gtfold-mfe/src/loader.cc index 5635739..1c39db9 100644 --- a/gtfold-mfe/src/loader.cc +++ b/gtfold-mfe/src/loader.cc @@ -17,54 +17,61 @@ along with this program. If not, see . */ -/* Modified by Amrita Mathuriya August 2007 - January 2009. 1) Functions are rewritten, removing calls of boost library functions and corrected bugs. - * This file defines various functions to read the thermodynamic parameters from files in the data directory. - * */ -/* Modified by Sonny Hernandez May 2007 - Aug 2007. All comments added marked by "SH: "*/ -/* Modified by Sainath Mallidi August 2009 - "*/ +#include +#include +#include +#include +#include -#include +#include #include + +#include +#include +#include +#include + +#include "data.h" +#include "utils.h" +#include "constants.h" +#include "global.h" #include "loader.h" -#include "main-c.h" #define xstr(s) str(s) #define str(s) #s -//#define GENBIN - using namespace std; -//Global Variables +std::string EN_DATADIR; + int poppen[5]; int maxpen; -int eparam[11]; /* Amrita: I am not sure of what does this array contain at different values.*/ -int multConst[3]; /* Amrita: I have copied multiloop penalties into this array */ -int dangle[4][4][4][2]; /* Dangling energies */ -int inter[31]; /* Size penalty for internal loops */ -int bulge[31]; /* Size penalty for bulges*/ -int hairpin[31]; /* Size penalty for hairpin loops */ -#if 0 -int stack[4][4][4][4]; -int tstkh[4][4][4][4]; -int tstki[4][4][4][4]; -#else -int stack[256]; /* Stacking energy for stack loops */ -int tstkh[256]; /* Terminal stacking energy for hairpin loops */ -int tstki[256]; /* Terminal stacking energy for internal loops */ -#endif +int eparam[11]; +int multConst[3]; /* for multiloop penalties. */ +int dangle[4][4][4][2]; /* Contain dangling energy values */ +int inter[31]; /* Contains size penalty for internal loops */ +int bulge[31]; /* Contain the size penalty for bulges */ +int hairpin[31]; /* Contains the size penalty for hairpin loops */ +int stack[256]; /* Stacking energy used to calculate energy of stack loops */ +int tstkh[256]; /* Terminal mismatch energy used in the calculations of hairpin loops */ +int tstki[256]; /* Terminal mismatch energy used in the calculations of internal loops */ int tloop[maxtloop + 1][2]; int numoftloops; -int iloop22[5][5][5][5][5][5][5][5]; /* 2*1 internal loops*/ int iloop21[5][5][5][5][5][5][5]; /* 2*1 internal loops */ -int iloop11[5][5][5][5][5][5]; /*1*1 internal loops */ -int coax[6][6][6][6]; -int tstackcoax[6][6][6][6]; -int coaxstack[6][6][6][6]; -int tstack[6][6][6][6]; -int tstkm[6][6][6][6]; - -int auend; /* For AU penalty */ +int iloop22[5][5][5][5][5][5][5][5]; /* 2*2 internal looops */ +int iloop11[5][5][5][5][5][5]; /* 1*1 internal loops */ + +//int coax[6][6][6][6]; +//int tstackcoax[6][6][6][6]; +//int coaxstack[6][6][6][6]; +//int tstack[6][6][6][6]; +//int tstkm[6][6][6][6]; + +int tstackm[5][5][6][6]; +int tstacke[5][5][6][6]; +int tstacki23[5][5][5][5]; + +int auend; int gubonus; int cint; /* cint, cslope, c3 are used for poly C hairpin loops */ int cslope; @@ -75,276 +82,183 @@ int efn2c; int triloop[maxtloop + 1][2]; int numoftriloops; int init; -int gail; -float prelog; /* Used for loops having size > 30 */ - -string EN_DATADIR; - -void populate(const char *userdatadir,bool userdatalogic) { - - cout << "Thermodynamic parameters: "; - -#ifndef GENBIN - if (!userdatalogic) { - EN_DATADIR.assign(xstr(DATADIR)); - EN_DATADIR += "/"; - EN_DATADIR += userdatadir; - } else { - EN_DATADIR.assign(userdatadir); - } -#else - EN_DATADIR = "data"; -#endif - - //Handle the ending forward slash case - if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') { - EN_DATADIR += "/"; - } - - - cout << EN_DATADIR << endl << endl; - - initMiscloopValues("miscloop.dat"); - // miscloop.dat - Miscellaneous loop file - initStackValues("stack.dat"); - // stack.dat - free energies for base pair stacking - initDangleValues("dangle.dat"); - // dangle.dat - single base stacking free energies - initLoopValues("loop.dat"); - // loop.dat - entropic component for internal, bulge and hairpin loops. - initTstkhValues("tstackh.dat"); - // tstackh.dat - free energies for terminal mismatch stacking in hairpin loops - initTstkiValues("tstacki.dat"); - // tstacki.dat - free energies for terminal mismatch stacking in internal loops - initTloopValues("tloop.dat"); - // tloop.dat - free energies for distinguished tetraloops - initInt21Values("int21.dat"); - // int21.dat - free energies for 2 x 1 interior loops - initInt22Values("int22.dat"); - // int22.dat - free energies for 2 x 2 interior loops - initInt11Values("int11.dat"); - // int11.dat - free energies for 1 x 1 interior loops -} - -char baseToDigit(std::string base) { - if (!strcmp(base.c_str(), "A")) { - return '1'; - } - if (!strcmp(base.c_str(), "C")) { - return '2'; - } - if (!strcmp(base.c_str(), "G")) { - return '3'; - } - if (!strcmp(base.c_str(), "U")) { - return '4'; - } - if (!strcmp(base.c_str(), "N")) { - return '5'; - } - return (char) NULL; +int gail; /* It is either 0 or 1. It is used for grosely asymmetric internal loops */ +float prelog; + +void readThermodynamicParameters(const char *userdatadir,bool userdatalogic, int unamode = 0, int rnamode = 0, int mismatch = 0) { + struct stat buf; + + if (!userdatalogic) { + std::string opt1, opt2, opt3; + char cwd[1024]; + bool found = false; + + opt1.assign(xstr(DATADIR)); + if (getenv("GTFOLDDATADIR") != 0) + opt2.assign(getenv("GTFOLDDATADIR")); + if (getcwd(cwd, sizeof(cwd)) != 0) { + opt3.assign(cwd); + opt3 += "/data"; + } + + if (stat(opt2.c_str(), &buf) == 0) { + found = true; + EN_DATADIR.assign(opt2); + fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', found \n"); + } else { + if (found == false) fprintf(stdout,"Checking for environ variable 'GTFOLDDATADIR', not found \n"); + } + + if (!found && stat(opt1.c_str(), &buf) == 0) { + found = true; + EN_DATADIR.assign(opt1); + fprintf(stdout,"Checking for default datadir '%s', found.\n", opt1.c_str()); + } else { + if (found == false) fprintf(stdout,"Checking for default datadir '%s', not found.\n", opt1.c_str()); + } + + if (!found && stat(opt3.c_str(), &buf) == 0){ + found = true; + EN_DATADIR.assign(opt3); + fprintf(stdout,"Checking under current dir '%s', found.\n", opt3.c_str()); + + } else { + if (found == false) fprintf(stdout,"Checking under current dir '%s', not found.\n", opt3.c_str()); + } + + EN_DATADIR += "/"; + if (found == false) { + exit(-1); + } + + if (unamode) { + EN_DATADIR += "UNAParams"; + }else if (rnamode) { + EN_DATADIR += "RNAParams"; + } else { + EN_DATADIR += "Turner99"; + } + } + else { + EN_DATADIR.assign(userdatadir); + if (stat(EN_DATADIR.c_str(), &buf) == -1){ + fprintf(stdout,"Checking for parameter files in dir '%s', not found.\n\n", EN_DATADIR.c_str()); + exit(-1); + } + } + + //Handle the ending forward slash case + if (EN_DATADIR[EN_DATADIR.length() - 1] != '/') { + EN_DATADIR += "/"; + } + + initMiscloopValues("miscloop.DAT", EN_DATADIR); + initDangleValues("dangle.DAT", EN_DATADIR); + initStackValues("stack.DAT", EN_DATADIR); + initLoopValues("loop.DAT", EN_DATADIR); + initTstkhValues("tstackh.DAT", EN_DATADIR); + initTstkiValues("tstacki.DAT", EN_DATADIR); + initTloopValues("tloop.DAT", EN_DATADIR); + + if (unamode) { + initInt21Values("asint1x2.DAT", EN_DATADIR); + initInt22Values("sint4.DAT", EN_DATADIR); + initInt11Values("sint2.DAT", EN_DATADIR); + initTstkmValues("tstackm.DAT", EN_DATADIR); + initTstkeValues("tstacke.DAT", EN_DATADIR); + initTstk23Values("tstacki23.DAT", EN_DATADIR); + } else if (mismatch) { + initTstkmValues("tstackm.DAT", EN_DATADIR); + initTstkeValues("tstacke.DAT", EN_DATADIR); + initInt21Values("int21.DAT", EN_DATADIR); + initInt22Values("int22.DAT", EN_DATADIR); + initInt11Values("int11.DAT", EN_DATADIR); + + } + else { + initInt21Values("int21.DAT", EN_DATADIR); + initInt22Values("int22.DAT", EN_DATADIR); + initInt11Values("int11.DAT", EN_DATADIR); + } } -unsigned char getBase(std::string base) { - //cout << base; - if (!strcmp(base.c_str(), "A") || !strcmp(base.c_str(), "a")) { - //cout << "1"; - return BASE_A; - } - if (!strcmp(base.c_str(), "C") || !strcmp(base.c_str(), "c")) { - //cout << "2"; - return BASE_C; - } - if (!strcmp(base.c_str(), "G") || !strcmp(base.c_str(), "g")) { - //cout << "3"; - return BASE_G; - } - if (!strcmp(base.c_str(), "U") || !strcmp(base.c_str(), "u") || !strcmp( - base.c_str(), "T") || !strcmp(base.c_str(), "t")) { - //cout << "4"; - return BASE_U; - } - if (!strcmp(base.c_str(), "N") || !strcmp(base.c_str(), "n")||!strcmp(base.c_str(), "R")|| !strcmp(base.c_str(), "r")|| !strcmp(base.c_str(), "Y")|| !strcmp(base.c_str(), "y")|| !strcmp(base.c_str(), "M")|| !strcmp(base.c_str(), "m")|| !strcmp(base.c_str(), "K")|| !strcmp(base.c_str(), "k")|| !strcmp(base.c_str(), "S")|| !strcmp(base.c_str(), "s")|| !strcmp(base.c_str(), "W")|| !strcmp(base.c_str(), "w")|| !strcmp(base.c_str(), "B")|| !strcmp(base.c_str(), "b")|| !strcmp(base.c_str(), "D")|| !strcmp(base.c_str(), "d")|| !strcmp(base.c_str(), "H")|| !strcmp(base.c_str(), "h")|| !strcmp(base.c_str(), "V")|| !strcmp(base.c_str(), "v")) { - //cout << "4"; - return BASE_A; - } - return 'X'; -} -unsigned char getBase1(std::string base) { - //cout << base; - if (!strcmp(base.c_str(), "A") || !strcmp(base.c_str(), "a")) { - //cout << "1"; - return BASE_A; - } - if (!strcmp(base.c_str(), "C") || !strcmp(base.c_str(), "c")) { - //cout << "2"; - return BASE_C; - } - if (!strcmp(base.c_str(), "G") || !strcmp(base.c_str(), "g")) { - //cout << "3"; - return BASE_G; - } - if (!strcmp(base.c_str(), "U") || !strcmp(base.c_str(), "u") || !strcmp( - base.c_str(), "T") || !strcmp(base.c_str(), "t")) { - //cout << "4"; - return BASE_U; - } - if (!strcmp(base.c_str(), "N") || !strcmp(base.c_str(), "n")|| !strcmp(base.c_str(), "R")|| !strcmp(base.c_str(), "r")|| !strcmp(base.c_str(), "Y")|| !strcmp(base.c_str(), "y")|| !strcmp(base.c_str(), "M")|| !strcmp(base.c_str(), "m")|| !strcmp(base.c_str(), "K")|| !strcmp(base.c_str(), "k")|| !strcmp(base.c_str(), "S")|| !strcmp(base.c_str(), "s")|| !strcmp(base.c_str(), "W")|| !strcmp(base.c_str(), "w")|| !strcmp(base.c_str(), "B")|| !strcmp(base.c_str(), "b")|| !strcmp(base.c_str(), "D")|| !strcmp(base.c_str(), "d")|| !strcmp(base.c_str(), "H")|| !strcmp(base.c_str(), "h")|| !strcmp(base.c_str(), "V")|| !strcmp(base.c_str(), "v")) { - //cout << "4"; - return 'N'; - } - return 'X'; -} +int initStackValues(const string& fileName, const string& dirPath) { + std::string filePath; + std::ifstream cf; -int initStackValues(string fileName) { + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; + if (!cf.good()) { + std::cerr << "File open failed - " << filePath << std::endl; + cf.close(); + exit(-1); + } - // Initialize the array with INFINITY - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 4; l++) { stack[fourBaseIndex(i,j,k,l)] = INFINITY_; } } } } - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // Read the thermodynamic parameters. - // The 24 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); - } - - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; - - while (i < 16) { - - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - ll = 0; - jj = 0; - - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; - } else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - stack[fourBaseIndex(ii,jj,kk,ll)] = temp; - r++; - z++; - if (r % 4 == 0) - jj++; - ll++; - if (ll == 4) - ll = 0; + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count/4; + k = count%4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + ss >> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + stack[fourBaseIndex(i,j,k,l)] = (int) floor(100.0 * atof(val.c_str()) + .5); } - } - i++; - if (!(i % 4)) - ii++; - - /* jj = 1; */ - kk = (i % 4); - + } + ++count; } - cf.close(); -#if 0 - cout << " Done!" << endl; -#endif + return 0; } -int initMiscloopValues(string fileName) { - /* - miscloop.dat - Miscellaneous loop file. Contains : - 1. Extrapolation for large loops based on polymer theory - 2. Asymmetric internal loop correction parameters. - 3. the f(m) array (see Ninio for details) - 4. Paremeters for multibranch loops - 5. Paremeters for multibranch loops (for efn2 only) - 6. Terminal AU or GU penalty - 7. Bonus for GGG hairpin - 8,9,10. C hairpin rules: a) slope b) intercept c) value for size 3 - 11. Intermolecular initiation free energy - 12. GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on or off) - */ +int initMiscloopValues(const string& fileName, const string& dirpath) { + std::string filePath; + std::ifstream cf; - char currentWord[256]; - string s; - ifstream cf; //cf = current file + filePath = dirpath + fileName; + cf.open(filePath.c_str(), ios::in); - fileName = EN_DATADIR + fileName; -#if 0 - cout << "Getting miscloop values from " << fileName << endl; -#endif - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); + if (!cf.good()) { + std::cerr << "File open failed - " << filePath << std::endl; + cf.close(); + exit(-1); } - s = ""; - cf >> currentWord; + char currentWord[256]; + std::string s; + for (int index = 1; index < 13; index++) { // There are total 12 values to read in. - while (strcmp(currentWord, "-->")) { - cf >> currentWord; - } if (index == 1) { cf >> currentWord; prelog = 100 * atof(currentWord); - //cout << "prelog = " << prelog << endl; } if (index == 2) { cf >> currentWord; maxpen = int(atof(currentWord) * 100.0 + .5); - //cout << "maxpen = " << maxpen << endl; } if (index == 3) { for (int count = 1; count <= 4; count++) { @@ -370,7 +284,6 @@ int initMiscloopValues(string fileName) { s = currentWord; multConst[count - 1] = (int) (atof(s.c_str()) * 100 + 0.5); eparam[table[count]] = (int) (atof(s.c_str()) * 100 + 0.5); - //cout << "\n multi " << multConst[count-1]; } } if (index == 5) { @@ -414,279 +327,86 @@ int initMiscloopValues(string fileName) { } } - cf.close(); + cf.close(); + return 0; } -int initMiscloopValuesOLD(string fileName) { - /* - miscloop.dat - Miscellaneous loop file. Contains : - 1. Extrapolation for large loops based on polymer theory - 2. Asymmetric internal loop correction parameters. - 3. the f(m) array (see Ninio for details) - 4. Paremeters for multibranch loops - 5. Paremeters for multibranch loops (for efn2 only) - 6. Terminal AU or GU penalty - 7. Bonus for GGG hairpin - 8,9,10. C hairpin rules: a) slope b) intercept c) value for size 3 - 11. Intermolecular initiation free energy - 12. GAIL Rule (Grossly Asymmetric Interior Loop Rule) (on or off) - */ +int initDangleValues(const std::string& fileName, + const std::string& dirPath) { + std::string filePath; + std::ifstream cf; - char currentWord[256]; - string s; - ifstream cf; //cf = current file - - fileName = EN_DATADIR + fileName; -#if 0 - cout << "Getting miscloop values from " << fileName << endl; -#endif - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - s = ""; + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - cf >> currentWord; - for (int index = 1; index < 13; index++) { // There are total 12 values to read in. - while (strcmp(currentWord, "-->")) { - cf >> currentWord; - } - if (index == 1) { - cf >> currentWord; - prelog = 100 * atof(currentWord); - cout << "prelog = " << prelog << endl; - } - if (index == 2) { - cf >> currentWord; - maxpen = int(atof(currentWord) * 100.0 + .5); - cout << "maxpen = " << maxpen << endl; - } - if (index == 3) { - for (int count = 1; count <= 4; count++) { - cf >> currentWord; - s = currentWord; - poppen[count] = (int) (atof(s.c_str()) * 100 + 0.5); - //cout << "poppen[" << count << "] = "<< poppen[count] << endl; - } - } - if (index == 4) { - eparam[1] = 0; - eparam[2] = 0; - eparam[3] = 0; - eparam[4] = 0; - eparam[7] = 30; - eparam[8] = 30; - eparam[9] = -500; - int table[4]; - table[1] = 5; - table[2] = 6; - table[3] = 10; - for (int count = 1; count <= 3; count++) { - cf >> currentWord; - s = currentWord; - eparam[table[count]] = (int) (atof(s.c_str()) * 100 + 0.5); - //printf(" %d ", eparam[table[count]]); - //cout << "eparam[" << table[count] << "] = "<< eparam[table[count]] << endl; - } - } - if (index == 5) { - int table[4]; - for (int count = 1; count <= 3; count++) { - cf >> currentWord; - s = currentWord; - table[count] = (int) (atof(s.c_str()) * 100 + 0.5); - //cout << "efn2[" << count << "] = "<< table[count] << endl; - } - efn2a = table[1]; - efn2b = table[2] - 1; - efn2c = table[3] - 1; - } - if (index == 6) { - cf >> currentWord; - auend = (int) (100 * atof(currentWord)); - //cout << "auend = " << auend << endl; - } - if (index == 7) { - cf >> currentWord; - gubonus = (int) (100 * atof(currentWord)); - //cout << "gubonus = " << gubonus << endl; - } - if (index == 8) { - cf >> currentWord; - cslope = (int) (100 * atof(currentWord)) + 1; - //cout << "cslope = " << cslope << endl; - } - if (index == 9) { - cf >> currentWord; - cint = (int) (100 * atof(currentWord)); - //cout << "cint = " << cint << endl; - } - if (index == 10) { - cf >> currentWord; - c3 = (int) (100 * atof(currentWord)) + 1; - //cout << "c3 = " << c3 << endl; - } - if (index == 11) { - cf >> currentWord; - init = (int) (100 * atof(currentWord)) + 1; - //cout << "init = " << init << endl; - } - if (index == 12) { - cf >> currentWord; - gail = (int) floor(.5 + atof(currentWord)); - //cout << "gail = " << gail << endl; - } - } - - cf.close(); -#if 0 - cout << " Done!" << endl; -#endif - return 0; -} - -int initDangleValues(string fileName) { - ifstream cf; //cf = current file - char currentLine[256]; - string currentString; - string s; - int index; - int i, j, k, l; - int ii, jj, kk, ll; // ii = 1st base, jj = 2nd base, kk = 3rd base, ll = 1 up or 2 low - - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 2; l++) { + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { dangle[i][j][k][l] = INFINITY_; } } } } + + int count = 0; - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - - // The 8 first lines are junk - for (index = 1; index <= 8; index++) { - cf.getline(currentLine, 256); - } - - // 8 lines of useful data - i = 0; - ii = 0; - jj = 0; - kk = 0; - ll = 0; - - while (i < 8) { - - if (i != 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); - - cf.getline(currentLine, 256); - s = currentLine; - j = 0; - - jj = 0; + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; - int z = 0; - int r = 0; - - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - kk++; - if (kk == 4) - kk = 0; - r++; - if (r % 4 == 0) - jj++; - } else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; + getline(cf, line); + ss << line; + if (line.empty()) continue; - int temp = (int) floor(100.0 * atof(value) + .5); - //if ( temp == 0 ) temp = -1; - dangle[ii][jj][kk][ll] = temp; - //cout<< "\n " << temp << " "<< ii <<" "<< jj << " "<< kk << " " << ll ; - r++; - z++; - if (r % 4 == 0) - jj++; - kk++; - if (kk == 4) - kk = 0; + i = count%4; + l = count/4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + j = cols/4; + ss >> val; + k = cols%4; + if (!(val == "inf")) { + dangle[i][j][k][l] = (int) floor(100.0 * atof(val.c_str()) + .5); } - - } - - i++; - ii++; - if (ii == 4) - ii = 0; - - if (i == 4) - ll = 1; - + } + ++count; } - cf.close(); - -#if 0 - cout << " Done!" << endl; -#endif + return 0; } -int initLoopValues(string fileName) { +int initLoopValues( const string& fileName, const string& dirPath) { // algorithm.c, line 2996 ifstream cf; // current file - char currentLine[256]; + std::string filePath; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + + //char currentLine[256]; char currentWord[256]; string s; - int index; + int index= 0; int tempValue = 0; -#if 0 - cout << "Getting loop values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } - // The 4 first lines are junk we don't need - for (index = 1; index <= 4; index++) { - cf.getline(currentLine, 256); - //s = currentLine; - //cout << s << endl; - } + while (index < 30) { for (int j = 1; j <= 4; j++) { cf >> currentWord; if (j == 1) index = atoi(currentWord); if (j > 1) { - if (strcmp(currentWord, ".")) { + if (strcmp(currentWord, "inf")) { tempValue = (int) (100 * atof(currentWord) + 0.5); } else { tempValue = INFINITY_; @@ -707,228 +427,224 @@ int initLoopValues(string fileName) { } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } -int initTstkhValues(string fileName) { - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; +int initTstk23Values(const std::string& fileName, const std::string& dirPath) { + int i1, j1, i2, j2; + std::string filePath; + std::ifstream cf; + std::string val; - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { - tstkh[fourBaseIndex(i,j,k,l)] = INFINITY_; - } - } - } - } + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } - // The 27 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); - } - - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; - - while (i < 16) { - - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); + for (i1 = 0; i1 < 5; ++i1) + for (i2 = 0; i2 < 5; ++i2) + for (j1 = 0; j1 < 5; ++j1) + for (j2 = 0; j2 < 5; ++j2) + if (i1 == 4 || j1 == 4) + tstacki23[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 4 || j2 == 4) + tstacki23[i1][j1][i2][j2] = 0; + else { + cf >> val; + tstacki23[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): + ((int) floor(100.0 * atof(val.c_str()) + .5)); + } + cf.close(); - cf.getline(currentLine, 256); - s = currentLine; - j = 0; + return 0; +} - ll = 0; - jj = 0; - int z = 0; - int r = 0; - while (s[z] != '\0') { - if (s[z] == ' ') - z++; +int initTstkeValues(const std::string& fileName, const std::string& dirPath) { + int i1, j1, i2, j2; + std::string filePath; + std::ifstream cf; + std::string val; - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; - } + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - else { - char value[10]; - int x = 0; + if (cf.fail()) { + cerr << "File open failed " << filePath << endl; + exit(-1); + } - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; + for (i1 = 0; i1 < 5; ++i1) { + for (i2 = 0; i2 < 6; ++i2) { + for (j1 = 0; j1 < 5; ++j1) { + for (j2 = 0; j2 < 6; ++j2) { + if (i1 == 4 || j1 == 4) + tstacke[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 5 || j2 == 5) + tstacke[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 4 || j2 == 4) + tstacke[i1][j1][i2][j2] = 0; + else { + cf >> val; + tstacke[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): + ((int) floor(100.0 * atof(val.c_str()) + .5)); + } } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - tstkh[fourBaseIndex(ii,jj,kk,ll)] = temp; - - r++; - z++; - if (r % 4 == 0) - jj++; - ll++; - if (ll == 4) - ll = 0; } - } - i++; - if (!(i % 4)) - ii++; - - jj = 0; - kk = (i % 4); - + } } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif + return 0; } -int initTstkiValues(string fileName) { - ifstream cf; //cf = current file - int i, j, k, l; - int ii, jj, kk, ll; - int index; - char currentLine[256]; - string currentString; - string s; - - for (i = 0; i < 4; i++) { - for (j = 0; j < 4; j++) { - for (k = 0; k < 4; k++) { - for (l = 0; l < 4; l++) { - tstki[fourBaseIndex(i,j,k,l)] = INFINITY_; - } - } - } - } +int initTstkmValues(const std::string& fileName, const std::string& dirPath) { + int i1, j1, i2, j2; + std::string filePath; + std::ifstream cf; + std::string val; - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } - // The 27 first lines are junk we don't need - for (index = 1; index <= 15; index++) { - cf.getline(currentLine, 256); + for (i1 = 0; i1 < 5; ++i1) { + for (i2 = 0; i2 < 6; ++i2) { + for (j1 = 0; j1 < 5; ++j1) { + for (j2 = 0; j2 < 6; ++j2) { + if (i1 == 4 || j1 == 4) + tstackm[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 5 || j2 == 5) + tstackm[i1][j1][i2][j2] = INFINITY_; + else if (i2 == 4 || j2 == 4) + tstackm[i1][j1][i2][j2] = 0; + else { + cf >> val; + tstackm[i1][j1][i2][j2] = (val == "inf")? (INFINITY_): + ((int) floor(100.0 * atof(val.c_str()) + .5)); + } + } + } + } } - i = 0; - kk = 0; - ii = 0; - jj = 0; - ll = 0; + cf.close(); - while (i < 16) { + return 0; +} - if (i % 4 == 0) - for (index = 1; index < 9; index++) - cf.getline(currentLine, 256); +int initTstkhValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; - cf.getline(currentLine, 256); - s = currentLine; - j = 0; + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - ll = 0; - jj = 0; + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { + tstkh[fourBaseIndex(i,j,k,l)] = INFINITY_; + } + } + } + } + + int count = 0; + + while (cf.good()) { + int i, j, k, l; + + std::string line; + std::stringstream ss; + + getline(cf, line); + ss << line; + if (line.empty()) continue; + + i = count/4; + k = count%4; + + for (int cols = 0; cols < 16; cols++) { + std::string val; + ss >> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + tstkh[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5); + } + } + ++count; + } + + return 0; +} - int z = 0; - int r = 0; - while (s[z] != '\0') { +int initTstkiValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; - if (s[z] == ' ') - z++; + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); - else if (s[z] == '.') { - z++; - ll++; - if (ll == 4) - ll = 0; - r++; - if (r % 4 == 0) - jj++; + for (int i = 0; i < 4; i++) { + for (int j = 0; j < 4; j++) { + for (int k = 0; k < 4; k++) { + for (int l = 0; l < 2; l++) { + tstki[fourBaseIndex(i,j,k,l)] = INFINITY_; + } } + } + } - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } + int count = 0; - value[x] = '\0'; + while (cf.good()) { + int i, j, k, l; - int temp = (int) floor(100.0 * atof(value) + .5); - tstki[fourBaseIndex(ii,jj,kk,ll)] = temp; + std::string line; + std::stringstream ss; - //cout << "\n temp " << temp << " " <> val; + j = cols/4; + l = cols%4; + if (!(val == "inf")) { + tstki[fourBaseIndex(i,j,k,l)]= (int) floor(100.0 * atof(val.c_str()) + .5); + } + } + ++count; } - cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } -//SH: Rewritten as an error was being generated by this function. -int initTloopValues(string fileName) { - ifstream cf; +int initTloopValues(const std::string& fileName, const std::string& dirPath) { + std::string filePath; + std::ifstream cf; + + filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + int count; char currentLine[256]; char currentSeqNumbers[7]; @@ -939,20 +655,6 @@ int initTloopValues(string fileName) { string s, temp; -#if 0 - cout << "Getting tloop values..."; -#endif - - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; - exit(-1); - } - // skip 2 lines - cf.getline(currentLine, 256); - cf.getline(currentLine, 256); - numoftloops = 0; while (!cf.eof() && (++(numoftloops) < maxtloop)) { @@ -965,34 +667,26 @@ int initTloopValues(string fileName) { while(currentLine[clindex]== ' ') clindex++; for (count = 0; count < 6; count++) { temp = currentLine[count + clindex]; - currentSeqNumbers[count] = baseToDigit(temp); - //cout << currentSeqNumbers[count]; - //cout << currentLine[count+1]; + currentSeqNumbers[count] = baseToDigit(temp.c_str()); } - //cout << endl; clindex=clindex+7; while(currentLine[clindex]== ' ') clindex++; count = 0; while(currentLine[clindex+count]!=' '&¤tLine[clindex+count]!='\0') { currentValue[count] = currentLine[count + clindex]; count++; - //cout << currentValue[count]; } - //cout << endl; - + tloop[numoftloops][0] = (int) atoi(currentSeqNumbers); - tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5); - //cout << " -- "<< tloop[numoftloops][0] << " | " << tloop[numoftloops][1] << endl; + + if (!(strcmp(currentValue,"inf")==0)) + tloop[numoftloops][1] = (int) floor(100.0 * atof(currentValue) + 0.5); } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } -int initInt22Values(string fileName) { - +int initInt22Values(const std::string& fileName, const std::string& dirPath) { //Read the 2x2 internal loops //key iloop22[a][b][c][d][j][l][k][m] = //a j l b @@ -1010,66 +704,36 @@ int initInt22Values(string fileName) { iloop22[i][j][k][r][q][t][y][z] = INFINITY_; ifstream cf; - int index, flag; char currentLine[256], currentValue[6]; - string s, s1, s2, temp; - string sre; int base[4]; int l, m; -#if 0 - cout << "Getting Int22 values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); - if (cf.fail()) { - cerr << "File open failed" << endl; + string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); + if (!cf.good()) { + cerr << "File open failed " << filePath << endl; exit(-1); } - // Get rid of the 38 1st lines - for (index = 1; index < 28; index++) { - cf.getline(currentLine, 256); - } - - sre = "Y"; - flag = 0; - - for (index = 1; index <= 36; index++) { // 36 tables 16x16 - // Go to the beginning of the tables - while (!flag) { - cf.getline(currentLine, 256); - - s = currentLine; - - int z = 0; - while (s[z] != '\0') { + const char* str[] = {"A-U","C-G","G-C","U-A","G-U","U-G"}; + - if (s[z] == 'Y') - flag = 1; + int outer, inner; - z++; - } - } - flag = 0; + for (int index = 1; index <= 36; index++) { // 36 tables 16x16 + std::stringstream ss1; + std::string s ; - // We skip 5 lines - for (i = 0; i < 5; ++i) { - cf.getline(currentLine, 256); - } - - // get the closing bases - cf.getline(currentLine, 256); - s1 = currentLine; - cf.getline(currentLine, 256); - s2 = currentLine; - s = s1 + s2; - - int z = 0; + outer = (index-1)/6; + inner = (index-1)%6; + ss1 << str[outer][0] << '-' << str[inner][0] << '-' << str[outer][2] << '-' << + str[inner][2]; + ss1 >> s; + int k = 0; + int z = 0; while (s[z] != '\0') { - if (s[z] == 'A') base[k++] = BASE_A; else if (s[z] == 'C') @@ -1078,22 +742,15 @@ int initInt22Values(string fileName) { base[k++] = BASE_G; else if (s[z] == 'U') base[k++] = BASE_U; - z++; } - cf.getline(currentLine, 256); - - //key iloop22[a][b][c][d][j][l][k][m] = - //a j l b - //c k m d - - for (int rowIndex = 1; rowIndex <= 16; rowIndex++) { + cf.getline(currentLine, 256); + std::stringstream ss; + ss << currentLine; for (int colIndex = 1; colIndex <= 16; colIndex++) { - cf >> currentValue; - // rowIndex = j*4+k - // colIndex = l*4+m + ss >> currentValue; j = ((rowIndex - 1) - (rowIndex - 1) % 4) / 4; k = (rowIndex - 1) % 4; @@ -1101,23 +758,18 @@ int initInt22Values(string fileName) { l = ((colIndex - 1) - (colIndex - 1) % 4) / 4; m = (colIndex - 1) % 4; - iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] - = (int) floor(100.0 * atof(currentValue) + 0.5); - //int temp = (int) floor(100.0*atof(currentValue)+0.5); - //printf("\n temp is : %d %d %d %d %d %d %d %d %d", temp, base[0], base[2], base[1], base[3], j, k, l, m ); + if (!(strcmp(currentValue,"inf")==0)) + iloop22[base[0]][base[1]][base[2]][base[3]][j][l][k][m] + = (int) floor(100.0 * atof(currentValue) + 0.5); } } } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif return 0; } -int initInt21Values(string fileName) { - +int initInt21Values(const std::string& fileName, const std::string& dirPath) { // 24x6 arrays of 4x4 values // c // a f @@ -1128,7 +780,7 @@ int initInt21Values(string fileName) { char currentLine[256]; string sre; string s, s1, s2; - int a, b, c, d, e, f, g, index; + int a, b, c, d, e, f, g; int i, j, k, r, q, t, y; int z; @@ -1165,87 +817,44 @@ int initInt21Values(string fileName) { base1[6] = BASE_U + 1; base2[6] = BASE_G + 1; - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); + std::string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed" << filePath << endl; exit(-1); } - // Get rid of the 18 1st lines - for (index = 1; index <= 17; index++) { - cf.getline(currentLine, 256); - } - i = 1; - while (i <= 6) { - j = 1; - while (j <= 4) { - k = 1; - - for (index = 1; index <= 10; index++) - cf.getline(currentLine, 256); - - s = currentLine; - while (k <= 4) { - cf.getline(currentLine, 256); - - s = currentLine; - r = 0; - z = 0; int jj = 1; d = 1; - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - d++; - if (d == 5) - d = 1; - r++; - if (r % 4 == 0) - jj++; - } - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; - - int temp = (int) floor(100.0 * atof(value) + .5); - a = base1[i]; - b = base2[i]; - f = base1[jj]; - g = base2[jj]; - c = k; - e = j; - - iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] - = temp; - //printf("\n temp %d, a %d , b %d, c %d, d %d, e %d, f %d, g %d", temp, a, b, c, d, e, f, g); - r++; - z++; - if (r % 4 == 0) - jj++; - d++; - if (d == 5) - d = 1; - } + std::stringstream ss; + ss << currentLine; + + for (z = 1; z <=24 ; z++) { + char value[32]; + ss >> value; + int temp = (int) floor(100.0 * atof(value) + .5); + a = base1[i]; + b = base2[i]; + f = base1[jj]; + g = base2[jj]; + c = k; + e = j; + + if (!(strcmp(value,"inf")==0)) + iloop21[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1][g - 1] = temp; + r++; + if (r % 4 == 0) jj++; + d++; + if (d == 5) d = 1; } k++; } @@ -1257,13 +866,8 @@ int initInt21Values(string fileName) { return 0; } -int initInt11Values(string fileName) { - - //Read the 1x1 internal loops - //key iloop11[a][b][c][d][j][l][k][m] = - //a b c - //d e f +int initInt11Values(const std::string& fileName, const std::string& dirPath) { int i, j, k, r, q, t; for (i = 0; i < 4; i++) @@ -1275,37 +879,20 @@ int initInt11Values(string fileName) { iloop11[i][j][k][r][q][t] = INFINITY_; ifstream cf; - int index; char currentLine[256]; string s; int base1[7]; int base2[7]; - //int j, k, l, m; int a, b, c, d, f; -#if 0 - cout << "Getting Int11 values..."; -#endif - fileName = EN_DATADIR + fileName; - cf.open(fileName.c_str(), ios::in); + std::string filePath = dirPath + fileName; + cf.open(filePath.c_str(), ios::in); if (cf.fail()) { - cerr << "File open failed" << endl; + cerr << "File open failed " << filePath << endl; exit(-1); } - // Get rid of the 19 1st lines - for (index = 1; index <= 17; index++) { - cf.getline(currentLine, 256); - } - - /* - Structure of the file: - array of 6x6 arrays - Order: - AU CG GC UA GU UG - */ - base1[1] = BASE_A + 1; base2[1] = BASE_U + 1; base1[2] = BASE_C + 1; @@ -1324,73 +911,42 @@ int initInt11Values(string fileName) { while (k < 6) { k++; - index = 0; - for (index = 1; index <= 10; index++) { - cf.getline(currentLine, 256); - } - i = 0; b = 1; while (i < 4) { - int jj = 1; ++i; cf.getline(currentLine, 256); - s = currentLine; - j = 0; int r = 0; - int z = 0; int e = 1; - while (s[z] != '\0') { - - if (s[z] == ' ') - z++; - - else if (s[z] == '.') { - z++; - e++; - if (e == 5) - e = 1; - r++; - if (r % 4 == 0) - jj++; - } - - else { - char value[10]; - int x = 0; - - while (s[z] != ' ' && s[z] != '\0') { - value[x++] = s[z++]; - } - - value[x] = '\0'; + std::stringstream ss; + ss << currentLine; - int temp = (int) floor(100.0 * atof(value) + .5); - a = base1[k]; - d = base2[k]; - c = base1[jj]; - f = base2[jj]; + for (int z=1; z <= 24; ++z) { + char value[32]; + ss >> value; + int temp = (int) floor(100.0 * atof(value) + .5); + a = base1[k]; + d = base2[k]; + c = base1[jj]; + f = base2[jj]; + + if (!(strcmp(value,"inf")==0)) iloop11[a - 1][b - 1][c - 1][d - 1][e - 1][f - 1] = temp; - r++; - z++; - if (r % 4 == 0) - jj++; - e++; - if (e == 5) - e = 1; - } + + r++; + if (r % 4 == 0) jj++; + e++; + if (e == 5) e = 1; } b++; } } cf.close(); -#if 0 - cout << " Done!" << endl; -#endif + return 0; } diff --git a/gtfold-mfe/src/main.cc b/gtfold-mfe/src/main.cc index 2dbc576..1689af9 100644 --- a/gtfold-mfe/src/main.cc +++ b/gtfold-mfe/src/main.cc @@ -1,799 +1,188 @@ /* -GTfold: compute minimum free energy of RNA secondary structure -Copyright (C) 2008 David A. Bader -http://www.cc.gatech.edu/~bader - -This program is free software: you can redistribute it and/or modify -it under the terms of the GNU General Public License as published by -the Free Software Foundation, either version 3 of the License, or -(at your option) any later version. - -This program is distributed in the hope that it will be useful, -but WITHOUT ANY WARRANTY; without even the implied warranty of -MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -GNU General Public License for more details. - -You should have received a copy of the GNU General Public License -along with this program. If not, see . -*/ - -/* Authored by Amrita Mathuriya August 2007 - January 2009.*/ -/* Modified by Sonny Hernandez May 2007 - Aug 2007. All comments added marked by "SH: "*/ -/* Modified by Sainath Mallidi August 2009 - "*/ + GTfold: compute minimum free energy of RNA secondary structure + Copyright (C) 2007-2011 David A. Bader, Christine E. Heitsch, + and Steve C. Harvey + http://www.cc.gatech.edu/~bader + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + */ -#include #include +#include #include #include #include #include -#include -#include #include #include #include #include -#include "loader.h" -#include "algorithms.h" -#include "algorithms-partition.h" -#include "traceback.h" -#include "subopt_traceback.h" #include "main.h" -#include "main-c.h" - -using namespace std; - -/* GLOBAL VARIABLES */ -enum BOOL NOISOLATE; -enum BOOL BPP; // calculating base pair probabilities -enum BOOL USERDATA; -enum BOOL PARAMS; -enum BOOL LIMIT_DISTANCE; -enum BOOL VERBOSE; - -int num_threads; -int LENGTH; -int contact_dist; - -unsigned char *RNA1; -unsigned char *RNA; /* Contains RNA string in terms of 0, 1, 2, 3 for A, C, G and U respectively*/ -int *structure; /* An array to contain the optimal structure */ -int *V; /* int V[LENGTH][LENGTH]; */ -int *W; -int **VBI; /* VBI(i,j) will contain the energy of optimal internal loop closed with (i,j) base pair */ -int **VM; /* VM(i, j) will contain the energy of optimla multiloop closed with (i,j) base pair */ -int **WM; /* This array is introduced to help multiloop calculations. WM(i,j) contains the optimal energy of string segment from si to sj if this forms part of a multiloop */ -int *indx; /* This array is used to index V array. Here V array is mapped from 2D to 1D and indx array is used to get the mapping back.*/ -int *constraints; - -double **QB; // QB[i][j] is the sum over all possible loops closed by (i,j), -// including the summed contributions of their subloops -double **Q; // Q[i][j] in addition to the above quantity QB[i][j], Q[i][j] -// also includes all configurations with (i,j) not paired -double **QM; // QM[i][j] is the sum of configuration energies from i to j, -// assuming that i,j are contained in a multiloop -double **P; // P[i][j] The probability that nucleotides i and j form a basepair - -/** - * Print the hep message and quit. - */ -void help() { - fprintf(stderr, - "Usage: gtfold [OPTION]... FILE\n\n"); - - fprintf(stderr, - " FILE is an RNA sequence file. Single line or FASTA formats are accepted.\n\n"); - - fprintf(stderr, "OPTIONS\n"); - fprintf(stderr, - " -c, --constraints FILE\n Load constraints from FILE. See Constraint syntax below\n"); - fprintf(stderr, - " -d, --limitCD num Set a maximum base pair contact distance to num. If no\n limit is given, base pairs can be over any distance\n"); - fprintf(stderr, - " -n, --noisolate Prevent isolated base pairs from forming\n"); - fprintf(stderr, - " -o, --output FILE Output to FILE (default output is to a .ct extension)\n"); - fprintf(stderr, - " -v, --verbose Run in versbose mode\n"); - - fprintf(stderr, - " -t, --threads num Limit number of threads used\n"); - fprintf(stderr, - " -h, --help Output help (this message) and exit\n"); - - fprintf(stderr, "\nBETA OPTIONS\n"); - fprintf(stderr, - " --bpp Calculate base pair probabilities\n"); - fprintf(stderr, - " --subopt range Calculate suboptimal structures within 'range' kcal/mol\n"); - fprintf(stderr, " of the mfe\n"); - - - fprintf(stderr, - "\nConstraint syntax:\n\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs\n\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); - exit(-1); -} - -/* Function for calculating time */ -double get_seconds() { - struct timeval tv; - gettimeofday(&tv, NULL); - return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0; -} - -/*Function for printing the sequence*/ -void printSequence(int len) { - int i = 1; - for (i = 1; i <= len; i++) { - if (RNA1[i] == 0) - printf("A"); - else if (RNA1[i] == 1) - printf("C"); - else if (RNA1[i] == 2) - printf("G"); - else if (RNA1 [i] == 3) - printf("T"); - else - printf("N"); - } - printf("\n"); -} - -/*Function for printing the input constraints*/ -void printConstraints(int len) { - int i = 1; - for (i = 1; i <= len; i++) { - if (constraints[i] > 0 && constraints[i] > i) - printf("("); - else if (constraints[i] > 0 && constraints[i] < i) - printf(")"); - else if (constraints[i] < 0) - printf("x"); - else - printf("."); - } - printf("\n"); -} - -/*Function for printing the predicted structure*/ -void printStructure(int len) { - int i = 1; - for (i = 1; i <= len; i++) { - if (structure[i] > 0 && structure[i] > i) - printf("("); - else if (structure[i] > 0 && structure[i] < i) - printf(")"); - else - printf("."); - } - printf("\n"); -} - -/* Initialize global variables. */ -void init_variables(int len) { - - int i; - - LENGTH = len + 1; - - RNA = (unsigned char *) malloc(LENGTH * sizeof(unsigned char)); - if (RNA == NULL) { - perror("Cannot allocate variable 'RNA'"); - exit(-1); - } - RNA1 = (unsigned char *) malloc(LENGTH * sizeof(unsigned char)); - if (RNA1 == NULL) { - perror("Cannot allocate variable 'RNA'"); - exit(-1); - } - structure = (int *) malloc(LENGTH * sizeof(int)); - if (structure == NULL) { - perror("Cannot allocate variable 'structure'"); - exit(-1); - } - - V = (int *) malloc(((LENGTH - 1) * (LENGTH) / 2 + 1) * sizeof(int)); - if (V == NULL) { - perror("Cannot allocate variable 'V'"); - exit(-1); - } - - W = (int *) malloc(LENGTH * sizeof(int)); - if (W == NULL) { - perror("Cannot allocate variable 'W'"); - exit(-1); - } - - VBI = (int **) malloc(LENGTH * sizeof(int *)); - if (VBI == NULL) { - perror("Cannot allocate variable 'VBI'"); - exit(-1); - } - for (i = 0; i < LENGTH; i++) { - VBI[i] = (int *) malloc(LENGTH * sizeof(int)); - if (VBI[i] == NULL) { - perror("Cannot allocate variable 'VBI[i]'"); - exit(-1); - } - } - - VM = (int **) malloc(LENGTH * sizeof(int *)); - if (VM == NULL) { - perror("Cannot allocate variable 'VM'"); - exit(-1); - } - for (i = 0; i < LENGTH; i++) { - VM[i] = (int *) malloc(LENGTH * sizeof(int)); - if (VM[i] == NULL) { - perror("Cannot allocate variable 'VM[i]'"); - exit(-1); - } - } - - WM = (int **) malloc(LENGTH * sizeof(int *)); - if (WM == NULL) { - perror("Cannot allocate variable 'WM'"); - exit(-1); - } - for (i = 0; i < LENGTH; i++) { - WM[i] = (int *) malloc(LENGTH * sizeof(int)); - if (WM[i] == NULL) { - perror("Cannot allocate variable 'WM[i]'"); - exit(-1); - } - } +#include "mfe_main.h" +#include "boltzmann_main.h" +#include "subopt_main.h" +#include "utils.h" +#include "global.h" - indx = (int *) malloc(LENGTH * sizeof(int)); - if (indx == NULL) { - perror("Cannot allocate variable 'indx'"); - exit(-1); - } - constraints = (int*) malloc((len + 1) * sizeof(int)); - if (constraints == NULL) { - perror("Cannot allocate variable 'constraints'"); - exit(-1); - } -} - -/* deallocate global variables */ -void free_variables() { - int i; - - free(indx); - for (i = 0; i < LENGTH; i++) - free(WM[i]); - free(WM); - for (i = 0; i < LENGTH; i++) - free(VM[i]); - free(VM); - for (i = 0; i < LENGTH; i++) - free(VBI[i]); - free(VBI); - free(W); - free(V); - free(constraints); - free(structure); - free(RNA); - free(RNA1); -} - -void init_partition_function_variables(int length) { - QB = mallocTwoD(length+1, length+1); - if(QB == NULL) { - fprintf(stderr,"Failed to allocate QB\n"); - exit(-1); - } - - Q = mallocTwoD(length+1, length+1); - if(Q == NULL) { - fprintf(stderr,"Failed to allocate Q\n"); - exit(-1); - } - - QM = mallocTwoD(length+1, length+1); - if(QM == NULL) { - fprintf(stderr,"Failed to allocate QM\n"); - exit(-1); - } - - P = mallocTwoD(length+1, length+1); - if(P == NULL) { - fprintf(stderr,"Failed to allocate P\n"); - exit(-1); - } -} - -void free_partition_function_variables(int length) { - freeTwoD(QB, length+1, length+1); - freeTwoD(Q, length+1, length+1); - freeTwoD(QM, length+1, length+1); - freeTwoD(P, length+1, length+1); -} - - -/* main function - This calls - * 1) Read command line arguments. - * 2) populate() from loader.cc to read the thermodynamic parameters defined in the files given in data directory. - * 3) Initialize variables - * 4) Calls calculate function defined in algorithms.c for filling up energy tables. - * 5) Calls trace function defined in trace.c file for tracing the optimal secondary structure - * 6) Then it generates .ct file from the 1D array structure. - * */ int main(int argc, char** argv) { - int i; - ifstream cf; - int length; - string s, seq; - int energy; - double t1; - NOISOLATE = FALSE; - BPP = FALSE; - VERBOSE = FALSE; - int delta = -1; - - fprintf(stdout, - "GTfold: A Scalable Multicore Code for RNA Secondary Structure Prediction\n"); - fprintf( - stdout, - "(c) 2007-2010 D.A. Bader, S. Mallidi, A. Mathuriya, C.E. Heitsch, S.C. Harvey\n"); - fprintf(stdout, "Georgia Institute of Technology\n\n"); - - /* Reading command line arguments */ - if (argc < 2) - help(); - - int fileIndex = 0, consIndex = 0, dataIndex = 0, lcdIndex = 0; - int rangeIndex = 0, thIndex = 0, outputFileIndex = 0; - - i = 1; - while (i < argc) { - if (argv[i][0] == '-') { - if (strcmp(argv[i], "--noisolate") == 0 || - strcmp(argv[i], "-n") == 0) { - NOISOLATE = TRUE; - } else if (strcmp(argv[i], "--output") == 0 || - strcmp(argv[i], "-o") == 0) { - if (i < argc) - outputFileIndex = ++i; - else - help(); - } else if (strcmp(argv[i], "--verbose") == 0 || - strcmp(argv[i], "-v") == 0) { - VERBOSE = TRUE; - } else if (strcmp(argv[i], "--help") == 0 || - strcmp(argv[i], "-h") == 0) { - help(); - } else if (strcmp(argv[i], "--constraints") == 0 || - strcmp(argv[i], "-c") == 0) { - if (i < argc) - consIndex = ++i; - else - help(); - } else if (strcmp(argv[i], "--threads") == 0 || - strcmp(argv[i], "-t") == 0) { - if (i < argc) - thIndex = ++i; - else - help(); - } else if (strcmp(argv[i], "--datadir") == 0) { - USERDATA = TRUE; - if (i < argc) - dataIndex = ++i; - else - help(); - } else if (strcmp(argv[i], "--limitCD") == 0 || - strcmp(argv[i], "-d") == 0) { - if (i < argc) - lcdIndex = ++i; - else - help(); - } else if (strcmp(argv[i], "--bpp") == 0) { - BPP = TRUE; - } else if (strcmp(argv[i], "--subopt") == 0) { - if (i> s; - seq.append(s); - s = ""; - } - s = seq; - - length = s.length(); - - init_variables(length); - - fprintf(stdout, "Sequence length: %5d\n\n", length); - - cf.close(); - - int **fbp = NULL, **pbp = NULL; - int numfConstraints = 0, numpConstraints = 0; - - if (consIndex != 0) { - int r = initialize_constraints(&fbp, &pbp, numpConstraints, numfConstraints, argv[consIndex]); - if (r == ERR_OPEN_FILE) { - free_variables(); - exit(-1); - } - else if (r == NO_CONS_FOUND) { - fprintf(stdout, "constraints file empty! Quitting...\n"); - exit(1); - } - } - - if (thIndex > 0) { - num_threads = atoi(argv[thIndex]); - } - - if (handle_IUPAC_code(s, length) == FAILURE) { - free_variables(); - exit(0); - } - - if(USERDATA==TRUE) - populate(argv[dataIndex],true); - else - populate("Turner99",false); /* Defined in loader.cc file to read in the thermodynamic parameter values from the tables in the ../data directory. */ - - initTables(length); /* Initialize global variables */ - - ///// Run Configuration Output ///// - - fprintf(stdout, "Run Configuration:\n"); - bool standardRun = TRUE; + print_header(); + + std::string cmd = argv[0]; + + if (cmd.find("gtmfe") != std::string::npos) { + mfe_main(argc, argv); + } else if (cmd.find("gtsubopt") != std::string::npos){ + subopt_main(argc,argv); + } else if (cmd.find("gtboltzmann") != std::string::npos) { + boltzmann_main(argc,argv); + } + + return EXIT_SUCCESS; +} - if (NOISOLATE == TRUE) { - fprintf(stdout, "- preventing isolated base pairs\n"); - standardRun = FALSE; - } + /* + if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { + printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); + exit(-1); + }*/ - if (consIndex != 0) { - fprintf(stdout, "- using constraint file: %s\n", argv[consIndex]); - standardRun = FALSE; - } + /* + //init_fold(seq); - contact_dist = length+1; - if (lcdIndex != 0) { - contact_dist = atoi(argv[lcdIndex]); - fprintf(stdout, "- maximum contact distance: %d\n", contact_dist); - standardRun = FALSE; - } - - if (BPP == TRUE) { - fprintf(stdout, "+ calculating base pair probabilities\n"); - standardRun = FALSE; - } - - if (rangeIndex != 0) { - delta = atoi(argv[rangeIndex]); - fprintf(stdout, "+ calculating suboptimal structures within %d kcal/mol of MFE\n", delta); - standardRun = FALSE; - } - - if(standardRun) - fprintf(stdout, "- standard\n"); - - ///// end run config output ///// - - - fprintf(stdout,"\nComputing minimum free energy structure ... \n\n"); - fflush(stdout); - - t1 = get_seconds(); - energy = calculate(length, fbp, pbp, numfConstraints, numpConstraints); - t1 = get_seconds() - t1; + // Read in thermodynamic parameters. Always use Turner99 data (for now) + if (SUBOPT_ENABLED) + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, 1, T_MISMATCH); + else + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); + + printRunConfiguration(seq); + + if (CALC_PART_FUNC == true) + { + printf("\nComputing partition function...\n"); + int pf_count_mode = 0; + if(PF_COUNT_MODE) pf_count_mode=1; + calculate_partition(seq.length(),pf_count_mode); + free_partition(); + //free_fold(seq.length()); + exit(0); + } + + if (RND_SAMPLE == true) + { + printf("\nComputing partition function...\n"); + int pf_count_mode = 0; + if(PF_COUNT_MODE) pf_count_mode=1; + double U = calculate_partition(seq.length(),pf_count_mode); + + batch_sample(num_rnd, seq.length(), U); + + free_partition(); + //free_fold(seq.length()); + exit(0); + } + + printf("\nComputing minimum free energy structure...\n"); + fflush(stdout); + + t1 = get_seconds(); + energy = calculate(seq.length()) ; + t1 = get_seconds() - t1; + + printf("Done.\n\n"); + printf("Results:\n"); + if (energy >= MAXENG) + printf("- Minimum Free Energy: %12.4f kcal/mol\n", 0.00); + else + printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00); + printf("- MFE runtime: %9.6f seconds\n", t1); - fprintf(stdout,"Minimum Free Energy: %9.2f\n", energy/100.00); - fprintf(stdout,"MFE runtime (seconds): %9.6f\n\n", t1); - if (rangeIndex != 0) - { - fprintf(stdout,"Computing suboptimal structures in range %d ...\n", delta); + if (SUBOPT_ENABLED) { t1 = get_seconds(); - // Traces the optimal structure - ss_map_t suboptdata = subopt_traceback(length, delta); + ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta); t1 = get_seconds() - t1; - fprintf(stdout,"Traceback runtime (seconds): %9.6f\n\n", t1); - - std::string suboptfile; - suboptfile += argv[fileIndex]; - - // if an extension exists, replace it with ct - if(suboptfile.find(".") != string::npos) - suboptfile.erase(suboptfile.rfind(".")); - suboptfile += ".struct"; - ofstream subopt_fp; + printf("\n"); + printf("Subopt traceback running time: %9.6f seconds\n", t1); - fprintf(stdout, "Writing suboptimal structures: %s\n", suboptfile.c_str()); - subopt_fp.open (suboptfile.c_str()); - - ss_map_t::iterator it; - for (it = suboptdata.begin(); it != suboptdata.end(); ++it) - subopt_fp << it->first << ' ' << it->second << std::endl; - - subopt_fp.close(); - - exit(0); - } - - // only fill the partition function structures if they are needed for BPP - if(BPP) { - fprintf(stdout,"Filling Partition Function structure... \n\n"); - fflush(stdout); - - // malloc the arrays - init_partition_function_variables(length); - - // fill the arrays - fill_partition_fn_arrays(length, QB, Q, QM); - - fprintf(stdout,"Q[1][n]: %f\n\n", Q[1][length]); - } - - - t1 = get_seconds(); - trace(length); /* Traces the optimal structure*/ - t1 = get_seconds() - t1; - - std::stringstream ss1, ss2; - - ss1 << length; - ss2 << energy/100.0; - - i = 0; - - // the output filename - string outputfile; - - // use given output file - if( outputFileIndex != 0) - outputfile += argv[outputFileIndex]; - - // or build off the input file - else { - outputfile += argv[fileIndex]; - - // if an extension exists, replace it with ct - if(outputfile.find(".") != string::npos) - outputfile.erase(outputfile.rfind(".")); - - outputfile += ".ct"; - } - - ofstream outfile; - outfile.open ( outputfile.c_str() ); - - fprintf(stdout, "Writing secondary structure: %s\n", outputfile.c_str()); - - outfile << length << "\t dG = " << energy/100.0; - i = 1; - while ( i <= length ) { - outfile << endl << i << "\t" << s[i-1] << "\t" << i-1 << "\t" << (i+1)%(length+1) << "\t" << structure[i] << "\t" << i; - i++; - } - outfile << endl; - outfile.close(); - - fprintf(stdout,"Traceback runtime (seconds): %9.6f\n\n", t1); - - printSequence(length); - if (consIndex != 0) { - printConstraints(length); + printf("Subopt structures saved in %s\n", suboptFile.c_str()); + save_subopt_file(suboptFile, subopt_data, seq, energy); + //free_fold(seq.length()); + exit(0); } - printStructure(length); - - if(BPP) { - fillBasePairProbabilities(length, structure, Q, QB, QM, P); - - printBasePairProbabilities(length, structure, P); - - free_partition_function_variables(length); - } - - free_variables(); - - return 0; -} - - -int initialize_constraints(int*** fbp, int ***pbp, - int& numpConstraints, int& numfConstraints, - const char* constr_file, enum BOOL verbose) { - ifstream cfcons; - - fprintf(stdout, "Running with constraints\n"); - fprintf(stdout, "Opening constraint file: %s\n", constr_file); - - cfcons.open(constr_file, ios::in); - if (cfcons != NULL) - fprintf(stdout, "Constraint file opened.\n"); - else { - fprintf(stderr, "Error opening constraint file\n\n"); - cfcons.close(); - return ERR_OPEN_FILE; //exit(-1); - } - - char cons[100]; - - while (!cfcons.eof()) { - cfcons.getline(cons, 100); - if (cons[0] == 'F' || cons[0] == 'f') - numfConstraints++; - if (cons[0] == 'P' || cons[0] == 'p') - numpConstraints++; - } - cfcons.close(); - - fprintf(stdout, "Number of Constraints given: %d\n\n", numfConstraints - + numpConstraints); - if (numfConstraints + numpConstraints != 0) - fprintf(stdout, "Reading Constraints.\n"); - else { - fprintf(stderr, "No Constraints found.\n\n"); - return NO_CONS_FOUND; - } - - *fbp = (int**) malloc(numfConstraints * sizeof(int*)); - *pbp = (int**) malloc(numpConstraints * sizeof(int*)); - - int fit = 0, pit = 0, it = 0; - - for (it = 0; it < numfConstraints; it++) { - (*fbp)[it] = (int*) malloc(2* sizeof (int)); - } - for(it=0; it tokens; -// tokenize(ncb1, tokens, ","); -// -// for (unsigned int i = 0; i < tokens.size(); ++i) { -// trim_spaces(tokens[i]); -// if (tokens.size() != 3 && tokens[i][1] != '-') -// // ignore -// continue; -// -// char b1 = getBase(tokens[i].substr(0,1)); -// char b2 = getBase(tokens[i].substr(2,1)); -// -// int r1=0; -// r1 = update_chPair(b1, b2); -// if (r1 == 1) -// printf("(%c,%c) ", tokens[i][0], tokens[i][2]) ; -// } -// printf("\n\n"); -//} +*/ + // release the malloc'd arrays + //free_fold(seq.length()); +/* + dangle_struct partition; + partition = malloc_partition_arrays_d(seq.length()); + fill_partition_arrays_d(partition); + printf("Done with the partition functioni.\n"); +*/ + //return EXIT_SUCCESS; +//} diff --git a/gtfold-mfe/src/mfe_main.cc b/gtfold-mfe/src/mfe_main.cc new file mode 100644 index 0000000..0525ea2 --- /dev/null +++ b/gtfold-mfe/src/mfe_main.cc @@ -0,0 +1,448 @@ +/* + GTfold: compute minimum free energy of RNA secondary structure + Copyright (C) 2007-2011 David A. Bader, Christine E. Heitsch, + and Steve C. Harvey + http://www.cc.gatech.edu/~bader + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see . + */ + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "main.h" +#include "mfe_main.h" +#include "utils.h" +#include "loader.h" +//#include "options.h" +#include "global.h" +#include "energy.h" +#include "algorithms.h" +#include "constraints.h" +#include "traceback.h" +#include "shapereader.h" + +using namespace std; + +static bool PARAM_DIR = false; +//static bool LIMIT_DISTANCE; +static bool CONS_ENABLED = false; +static bool VERBOSE = false; +static bool SHAPE_ENABLED = false; +static bool T_MISMATCH = false; +static bool UNAMODE = false; +static bool RNAMODE = false; +static bool b_prefilter = false; + +static string seqfile = ""; +static string constraintsFile = ""; +static string outputPrefix = ""; +static string outputFile = ""; +static string outputDir = ""; +static string shapeFile = ""; +static string paramDir; // default value + +static int dangles=-1; +static int prefilter1=2; +static int prefilter2=2; + +static int nThreads = -1; +static int contactDistance = -1; + +static void help(); +void printRunConfiguration(string seq); +void parse_mfe_options(int argc, char** argv); + +void init_fold(const char* seq) { + assert(seq != NULL); + int len = strlen(seq); + + init_global_params(len); + + if (!encodeSequence(seq)) { + free_fold(len); + exit(0); + } + + create_tables(len); + + if (CONS_ENABLED) { + init_constraints(constraintsFile.c_str(), len); + } + + if (SHAPE_ENABLED) { + readSHAPEarray(shapeFile.c_str(),len); + } + + if (UNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --unafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --unafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --unafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --unafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + + if (RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using --rnafold\n"); + if (PARAM_DIR) printf("Ignoring -p option, using --rnafold\n"); + if (dangles == 0 || dangles == 2) + printf("Ignoring -d option, using --rnafold\n"); + if (b_prefilter == 1) + printf("Ignoring --prefilter option, using --rnafold\n"); + T_MISMATCH = false; + PARAM_DIR = false; + dangles = -1; + b_prefilter = false; + } + + if ((dangles == 0 || dangles == 2) && !UNAMODE && !RNAMODE) { + if (T_MISMATCH) printf("Ignoring -m option, using -d option\n"); + T_MISMATCH = false; + } else { + if (dangles != -1 && !UNAMODE && !RNAMODE) printf("Ignoring -d as it accept 0 or 2 only\n"); + dangles = -1; + } + + g_nthreads = nThreads; + g_unamode = UNAMODE; + g_mismatch = T_MISMATCH; + g_verbose = VERBOSE; + g_prefilter_mode = b_prefilter; + g_prefilter1 = prefilter1; + g_prefilter2 = prefilter2; + g_dangles = dangles; + +#ifdef DEBUG + printf("g_nthreads = %d\n", g_nthreads); + printf("g_unamode = %d\n", g_unamode); + printf("g_mismatch = %d\n", g_mismatch); + printf("g_prefilter_mode = %d\n", g_prefilter_mode); + printf("g_dangles = %d\n", g_dangles); + +#endif + +} + +void free_fold(int len) { + if (CONS_ENABLED) + free_constraints(len); + if (SHAPE_ENABLED){ + free_shapeArray(len); + } + + free_tables(len); + free_global_params(); +} + + +int mfe_main(int argc, char** argv) { + std::string seq; + int energy; + + parse_mfe_options(argc, argv); + + if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { + printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); + exit(-1); + } + + init_fold(seq.c_str()); + + // Read in thermodynamic parameters. Always use Turner99 data (for now) + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, UNAMODE, RNAMODE, T_MISMATCH); + printRunConfiguration(seq); + + printf("\nComputing minimum free energy structure...\n"); + fflush(stdout); + + double t1 = get_seconds(); + energy = calculate(seq.length()) ; + t1 = get_seconds() - t1; + + printf("Done.\n\n"); + printf("Results:\n"); + if (energy >= MAXENG) + printf("- Minimum Free Energy: %12.4f kcal/mol\n", 0.00); + else + printf("- Minimum Free Energy: %12.4f kcal/mol\n", energy/100.00); + printf("- MFE runtime: %9.6f seconds\n", t1); + + t1 = get_seconds(); + trace(seq.length()); + t1 = get_seconds() - t1; + + printf("\n"); + print_sequence(seq.length()); + print_structure(seq.length()); + + if (CONS_ENABLED) + print_constraints(seq.length()); + + if (SHAPE_ENABLED && VERBOSE) + print_shapeArray(seq.length()); + + save_ct_file(outputFile, seq, energy); + printf("\nMFE structure saved in .ct format to %s\n", outputFile.c_str()); + + if(CONS_ENABLED && VERBOSE){ + printf("Verifying that structure fulfills constraint criteria... "); + if(verify_structure()){ + printf("OK\n"); + } + else{ + printf("ERROR: NOT OK!!\n"); + fprintf(stderr, "ERROR: Structure does not fulfill constraint criteria.\n"); + fprintf(stderr, "Structure file: %s\n", outputFile.c_str()); + fprintf(stderr, "Constraint file: %s\n", constraintsFile.c_str()); + } + } + + free_fold(seq.length()); + + return EXIT_SUCCESS; +} + + +void parse_mfe_options(int argc, char** argv) { + int i; + + for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) { + //LIMIT_DISTANCE = true; + enable_limit_distance(true); + set_contact_distance(contactDistance); + } + else + help(); + } + else + help(); + }else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + T_MISMATCH = true; + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + prefilter1 = atoi(argv[++i]); + if (prefilter1 <= 0 ) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter2 = prefilter1; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } + + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } + + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; + + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } + + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + +} + + +void printRunConfiguration(string seq) { + bool standardRun = true; + + printf("Run Configuration:\n"); + if (RNAMODE == true) { + printf("+ running in rnafold mode\n"); + standardRun = false; + } + if (UNAMODE == true) { + printf("+ running in unafold mode\n"); + standardRun = false; + } + if (dangles == 0 || dangles == 2) { + printf("+ running in dangle %d mode\n", dangles); + standardRun = false; + } + if (T_MISMATCH == true) { + printf("+ enabled terminal mismatch calculations\n"); + standardRun = false; + } + if (b_prefilter == true) { + printf("+ running with prefilter value = %d\n",prefilter1); + standardRun = false; + } + + if(!constraintsFile.empty()) { + printf("- using constraint file: %s\n", constraintsFile.c_str()); + standardRun = false; + } + + if(!shapeFile.empty()){ + printf("- using SHAPE data file: %s\n", shapeFile.c_str()); + } + if (contactDistance != -1) { + printf("- maximum contact distance: %d\n", contactDistance); + standardRun = false; + } + + if(standardRun) + printf("- standard\n"); + + printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str()); + printf("- input file: %s\n", seqfile.c_str()); + printf("- sequence length: %d\n", (int)seq.length()); + printf("- output file: %s\n", outputFile.c_str()); +} + +static void help() { + printf("Usage: gtmfe [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + printf(" -c, --constraints FILE\n"); + printf(" Load constraints from FILE. See Constraint syntax below.\n"); + printf(" -d, --dangle INT Restricts treatment of dangling energies (INT=0,2),\n"); + printf(" see below for details.\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); + printf(" limit is given, base pairs can be over any distance.\n"); + printf(" -m --mismatch Enable terminal mismatch calculations\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming.\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -t, --threads INT Limit number of threads used to INT.\n"); + printf(" -v, --verbose Run in verbose mode (includes loop-by-loop energy decomposition\n"); + printf(" and confirmation of constraints satisfied).\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); + printf(" neighboring nucleotides such that it could be part of\n"); + printf(" a helix of length INT.\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5).\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8), subject to traceback\n"); + printf(" implementation.\n"); + + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); + + printf("\nConstraint syntax:\n"); + printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); + + printf("\nDangle:\n"); + printf("\tINT=0 ignores dangling energies (mostly for debugging).\n"); + printf("\tINT=2 dangling energies are added for nucleotides on either\n"); + printf("\tside of each branch in multi-loops and external loops.\n"); + printf("\tAll other values for INT are ignored.\n"); + exit(-1); +} + diff --git a/gtfold-mfe/src/options.cc b/gtfold-mfe/src/options.cc new file mode 100644 index 0000000..30889de --- /dev/null +++ b/gtfold-mfe/src/options.cc @@ -0,0 +1,328 @@ +#include "loader.h" +#include "options.h" + +#include + +using namespace std; + +bool ILSA; +bool NOISOLATE; +bool PARAM_DIR = false; +bool LIMIT_DISTANCE; +bool BPP_ENABLED; +bool SUBOPT_ENABLED; +bool CONS_ENABLED = false; +bool VERBOSE = false; +bool SHAPE_ENABLED = false; +bool T_MISMATCH = false; +bool UNAMODE = false; +bool RNAMODE = false; +bool b_prefilter = false; +bool CALC_PART_FUNC = false; +bool RND_SAMPLE = false; +bool PF_COUNT_MODE = false; + +string seqfile = ""; +string constraintsFile = ""; +string outputPrefix = ""; +string outputFile = ""; +string suboptFile = ""; +string bppOutFile = ""; +string outputDir = ""; +string shapeFile = ""; +string paramDir; // default value + +int num_rnd = 0; +int dangles=-1; +int prefilter1=2; +int prefilter2=2; + +float suboptDelta = 0.0; +int nThreads = -1; +int contactDistance = -1; + +/** + * Print the help message and quit. + */ + +/* +void help() { + printf("Usage: gtfold [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + printf(" -c, --constraints FILE\n"); + printf(" Load constraints from FILE. See Constraint syntax below.\n"); + printf(" -d, --dangle INT Restricts treatment of dangling energies (INT=0,2),\n"); + printf(" see below for details.\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -l, --limitCD INT Set a maximum base pair contact distance to INT. If no\n"); + printf(" limit is given, base pairs can be over any distance.\n"); + printf(" -m --mismatch Enable terminal mismatch calculations\n"); +// printf(" -n, --noisolate Prevent isolated base pairs from forming.\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -t, --threads INT Limit number of threads used to INT.\n"); + printf(" -v, --verbose Run in verbose mode (includes loop-by-loop energy decomposition\n"); + printf(" and confirmation of constraints satisfied).\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + printf(" --prefilter INT Prohibits any basepair which does not have appropriate\n"); + printf(" neighboring nucleotides such that it could be part of\n"); + printf(" a helix of length INT.\n"); + printf(" --rnafold Run as RNAfold default mode (ViennaPackage version 1.8.5).\n"); + printf(" --unafold Run as UNAfold default mode (version 3.8), subject to traceback\n"); + printf(" implementation.\n"); + + printf("\nBETA OPTIONS\n"); + printf(" --bpp Calculate base pair probabilities.\n"); + printf(" --partition Calculate the partition function.\n"); + printf(" --pf_count Calculate the structure count using partition function and zero energy value.\n"); + printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); + printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); + printf(" -s, --useSHAPE FILE Use SHAPE constraints from FILE.\n"); + + printf("\nConstraint syntax:\n"); + printf("\tF i j k # force (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i j k # prohibit (i,j)(i+1,j-1),.......,(i+k-1,j-k+1) pairs.\n"); + printf("\tP i 0 k # make bases from i to i+k-1 single stranded bases.\n"); + + printf("\nDangle:\n"); + printf("\tINT=0 ignores dangling energies (mostly for debugging).\n"); + printf("\tINT=2 dangling energies are added for nucleotides on either\n"); + printf("\tside of each branch in multi-loops and external loops.\n"); + printf("\tAll other values for INT are ignored.\n"); + exit(-1); +} +*/ + +/** + * Parse the options from argc and argv and save them into global state. + */ +/* +void parse_options(int argc, char** argv) { + int i; + + for(i=1; i= 0 && !strcmp(ss.str().c_str(),argv[i])) + LIMIT_DISTANCE = true; + else + help(); + } + else + help(); + } else if(strcmp(argv[i], "--noisolate") == 0 || strcmp(argv[i], "-n") == 0) { + NOISOLATE = true; + } else if(strcmp(argv[i], "--prefix") == 0 || strcmp(argv[i], "-o") == 0) { + if(i < argc) + outputPrefix = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--workdir") == 0 || strcmp(argv[i], "-w") == 0) { + if(i < argc) + outputDir = argv[++i]; + else + help(); + } else if (strcmp(argv[i], "--paramdir") == 0 || strcmp(argv[i], "-p") == 0) { + if(i < argc) { + paramDir = argv[++i]; + PARAM_DIR = true; + } + else + help(); + } else if (strcmp(argv[i], "--dangle") == 0 || strcmp(argv[i], "-d") == 0) { + std::string cmd = argv[i]; + if(i < argc) { + dangles = atoi(argv[++i]); + if (!(dangles == 0 || dangles == 2)) { + dangles = -1; + printf("Ignoring %s option as it accepts either 0 or 2\n", cmd.c_str()); + } + } else + help(); + } else if (strcmp(argv[i], "-m") == 0 || strcmp(argv[i], "--mismatch") == 0) { + T_MISMATCH = true; + } else if (strcmp(argv[i], "--unafold") == 0) { + UNAMODE = true; + } else if (strcmp(argv[i], "--rnafold") == 0) { + RNAMODE = true; + } else if (strcmp(argv[i], "--prefilter") == 0) { + if(i < argc) { + prefilter1 = atoi(argv[++i]); + if (prefilter1 <= 0 ) { + printf("INVALID ARGUMENTS: --prefilter accepts positive integers\n\n"); + help(); + } + b_prefilter = true; + prefilter2 = prefilter1; + } else + help(); + } + else if(strcmp(argv[i], "--threads") == 0 || strcmp(argv[i], "-t") == 0) { + if(i < argc) + nThreads = atoi(argv[++i]); + else + help(); + } else if (strcmp(argv[i], "--verbose") == 0 || strcmp(argv[i], "-v") == 0) { + VERBOSE = true; + } + else if(strcmp(argv[i], "--bpp") == 0) { + BPP_ENABLED = true; + } else if(strcmp(argv[i], "--subopt") == 0) { + SUBOPT_ENABLED = true; + dangles = 2; + if(i < argc) + suboptDelta = atof(argv[++i]); + else + help(); + } else if (strcmp(argv[i],"--partition") == 0) { + CALC_PART_FUNC = true; + } else if (strcmp(argv[i],"--pf_count") == 0) { + CALC_PART_FUNC = true; + PF_COUNT_MODE = true; + } else if (strcmp(argv[i],"--sample") == 0) { + RND_SAMPLE = true; + if(i < argc) + num_rnd = atoi(argv[++i]); + else + help(); + } + else if (strcmp(argv[i], "--useSHAPE") == 0){ + if( i < argc){ + shapeFile = argv[++i]; + SHAPE_ENABLED = true; + } + else + help(); + } + } else { + seqfile = argv[i]; + } + } + + // Must have an input file specified + if(seqfile.empty()) { + help(); + printf("Missing input file.\n"); + } + + // If no output file specified, create one + if(outputPrefix.empty()) { + // base it off the input file + outputPrefix += seqfile; + + size_t pos; + // extract file name from the path + if ((pos=outputPrefix.find_last_of('/')) > 0) { + outputPrefix = outputPrefix.substr(pos+1); + } + + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + bppOutFile += outputDir; + bppOutFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; + + bppOutFile += outputPrefix; + bppOutFile += "_bpp.txt"; +} +*/ +/** + * Prints the run configuration for this run. + * + * The lines that start with a '-' are normal options, the '+' are beta options. + */ +/* +void printRunConfiguration(string seq) { + bool standardRun = true; + + printf("Run Configuration:\n"); + if (RNAMODE == true) { + printf("+ running in rnafold mode\n"); + standardRun = false; + } + if (UNAMODE == true) { + printf("+ running in unafold mode\n"); + standardRun = false; + } + if (dangles == 0 || dangles == 2) { + printf("+ running in dangle %d mode\n", dangles); + standardRun = false; + } + if (T_MISMATCH == true) { + printf("+ enabled terminal mismatch calculations\n"); + standardRun = false; + } + if (b_prefilter == true) { + printf("+ running with prefilter value = %d\n",prefilter1); + standardRun = false; + } + if (NOISOLATE == true) { + printf("- preventing isolated base pairs\n"); + standardRun = false; + } + + if(!constraintsFile.empty()) { + printf("- using constraint file: %s\n", constraintsFile.c_str()); + standardRun = false; + } + + if(!shapeFile.empty()){ + printf("- using SHAPE data file: %s\n", shapeFile.c_str()); + } + if (contactDistance != -1) { + printf("- maximum contact distance: %d\n", contactDistance); + standardRun = false; + } + + if (BPP_ENABLED == true) { + printf("+ calculating base pair probabilities\n"); + printf("+ BPP output file: %s\n", bppOutFile.c_str()); + standardRun = false; + } + + if (SUBOPT_ENABLED) { + printf("+ calculating suboptimal structures within %f kcal/mol of MFE\n", suboptDelta); + printf("+ suboptimal structures file: %s\n", suboptFile.c_str()); + standardRun = false; + } + + if(standardRun) + printf("- standard\n"); + + printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str()); + printf("- input file: %s\n", seqfile.c_str()); + printf("- sequence length: %d\n", (int)seq.length()); + printf("- output file: %s\n", outputFile.c_str()); +} +*/ diff --git a/gtfold-mfe/src/partition-dangle.c b/gtfold-mfe/src/partition-dangle.c new file mode 100644 index 0000000..df677fc --- /dev/null +++ b/gtfold-mfe/src/partition-dangle.c @@ -0,0 +1,197 @@ +//Attempting to follow Ding and Lawrence as closely as possible + +/**s1 -> partial_external +* s2 -> partial_multi +* s3 -> partial_multi2 +* u1 -> u_multi +* f -> cond_dangle (conditional) +* ebi -> eL +**/ + +#include +#include + +#include "energy.h" +#include "utils.h" +#include "global.h" +#include "data.h" +#include "algorithms-partition.h" +#include "partition-dangle.h" + +#define MIN_TURN 4 +#define MAX_LOOP 30 + +//double RT = (0.00198721 * 310.15)/100.00; + +double cond_dangle(int j, int h, int l){ + if(j - 1 == l) + return 1; + else + return exp(-Ed3(h,l,l+1)/RT); +} + +dangle_struct malloc_partition_arrays_d(int length){ + dangle_struct ret_struct; + ret_struct.length = length; + + //Add 1 since we're not zero indexed + ret_struct.u = mallocTwoD(length + 1, length + 1); + ret_struct.up = mallocTwoD(length + 1, length + 1); + ret_struct.upm = mallocTwoD(length + 1, length + 1); + ret_struct.u1 = mallocTwoD(length + 1, length + 1); + ret_struct.s1 = mallocTwoD(length + 1, length + 1); + ret_struct.s2 = mallocTwoD(length + 1, length + 1); + ret_struct.s3 = mallocTwoD(length + 1, length + 1); + + int i,j; + + for(i = 0; i < length + 1; i++){ + for(j = 0; j < length + 1; j++){ + ret_struct.u[i][j] = 1; + ret_struct.up[i][j] = 0; + ret_struct.upm[i][j] = 0; + ret_struct.u1[i][j] = 0; + ret_struct.s1[i][j] = 0; + ret_struct.s2[i][j] = 0; + ret_struct.s3[i][j] = 0; + } + } + return ret_struct; +} + +void free_partition_arrays_d(struct partition_d part) +{ + freeTwoD(part.u, part.length, part.length); + freeTwoD(part.up, part.length, part.length); + freeTwoD(part.upm, part.length, part.length); + freeTwoD(part.u1, part.length, part.length); + freeTwoD(part.s1, part.length, part.length); + freeTwoD(part.s2, part.length, part.length); + freeTwoD(part.s3, part.length, part.length); +} + +void fill_partition_arrays_d(dangle_struct part_struct){ + //So that we don't have the /100 in every exponent + //Seeing as we missed some last time + + double ** partial_external = part_struct.s1; + double ** partial_multi = part_struct.s2; + double ** partial_multi2 = part_struct.s3; + double ** u_multi = part_struct.u1; + double ** u = part_struct.u; + double ** up = part_struct.up; + double ** upm = part_struct.upm; + int len = part_struct.length; + + int seg_length; + int i,j; + + for(seg_length = MIN_TURN; seg_length <= len; len++){ + //Insert parallelism here. + for(i = 1; i < len - seg_length; i++){ + j = i + seg_length - 1; + + int l; + if(canPair(i,j)){ + for(l = i+2; l < j; l++){ + upm[i][j] += up[i+1][l] * exp(-(Ea + 2 * Ec + auPenalty(i + 1,l)/RT)) * + (exp(-Ed3(i + 1,l,l+1)/RT) * u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + if(l != i+2){ //goes from i + 2 < l < j + upm[i][j] += up[i + 2][l] * + exp(-(Ea + 2 * Ec + Eb + Ed3(j,i,i + 1) + auPenalty(i + 2, l))/RT) * + (exp(-Ed3(i + 2,l,l + 1)/RT)*u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + + if(l != j - 1){ + upm[i][j] += exp(-Ed3(j,i,i + 1)/RT)*exp(-(Ea + 2 * Ec + (l - i - 1) * Eb)/RT) * + partial_multi[l][j]; + //Changed h in the paper to l it makes no difference + //other than unifying loops + } + } + } + + + up[i][j] += exp(-eH(i,j)/RT) + exp(-eS(i,j)/RT) * up[i + 1][j - 1] + upm[i][j]; + for(l = j - 1; l > i + 1; l--){ + if((j - l) - 2> MAX_LOOP){ + break; + } + int h; + for(h = i + 1 ; h < l; h++){ + if(!(i == h - 1 && j == l - 1)){ //If this is true we have a stack + up[i][j] += exp(-eL(i,j,h,l)/RT); + } + if((j - l) + (h - i) - 2 > MAX_LOOP){ + break; + } + } + } + }//End checkpair conditional + + for(l = i + 1; l <= j ; l++){ + u_multi[i][j] += up[i][l] * exp(-(Ec + auPenalty(i,l))/RT) * + (cond_dangle(j + 1,i,l) * exp(-(j - l) * Eb/RT) + + exp(-Ed3(i,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + if(l != i+1){ + u_multi[i][j] += up[i + 1][j]*exp(-(Ec + Eb + auPenalty(i + 1,l))/RT)* + (cond_dangle(j + 1, i + 1, l) * exp(-(j - l)*Eb/RT) + + exp(-Ed3(i + 1,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + if(l != j){ + u_multi[i][j] += exp(-(Ec + (l - i) * Eb)/RT) * partial_multi2[l][j]; + + } + } + } + + + int h = i; //To stay consistant with the notation in the paper. + + for(l = h+1; l < j; l++){ + partial_external[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (exp(-Ed3(h,l,l + 1)/RT)*u[l + 2][j - 1] + + u[l + 1][j] - + u[l + 2][j]); + + partial_multi[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j - 1] + + u_multi[l + 1][j - 1] - + u_multi[l + 2][j - 1]); + + partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (cond_dangle(j + 1, h, l)*exp(-(j - l) * Eb / RT) + + exp(-Ed3(h,l,l + 1)/RT)*u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + + } + /** partial_multi2 goes up to j **/ + partial_multi2[h][j] += up[h][l] * exp( -(Ed5(h,l,h - 1) + auPenalty(h,l)) / RT) * + (cond_dangle(j + 1, h, l)*exp(-(j-l) * Eb / RT) + + exp(-Ed3(h,l,l + 1)/RT) * u_multi[l + 2][j] + + u_multi[l + 1][j] - + u_multi[l + 2][j]); + + //Finally we do the u matrix + u[i][j] = 1 + up[i][j]*exp(-auPenalty(i,j) /RT); + + for(l = i + 1; l < j; l++){ + //Replaced l with h in the next line to unify loops + u[i][j] += up[l][j] * exp(-(Ed5(l, j , l - 1) + auPenalty(h,j))/RT); + + u[i][j] += exp(-(auPenalty(i,l))/RT)*(exp(-Ed3(i,l,l + 1)/RT) * u[l + 2][j] + + u[l + 1][j] - u[l + 2][j]); + if(l != j - 1) { + u[i][j] += partial_external[l][j]; + } + } + }//end of minor (paralellizeable) for loop + }//End of major for loop +} diff --git a/gtfold-mfe/src/partition-func.c b/gtfold-mfe/src/partition-func.c new file mode 100644 index 0000000..4547364 --- /dev/null +++ b/gtfold-mfe/src/partition-func.c @@ -0,0 +1,820 @@ +#include +#include +#include +#include "partition-func.h" +#include "energy.h" +#include "algorithms-partition.h" +#include "global.h" +#include "utils.h" +#include +//#include "options.h" + +double ** u; +double ** up; +double ** upm; +double ** ud; +double ** u1d; + +double ** s1; +double ** s2; +double ** s3; +double ** u1; + +int part_len; +int PF_COUNT_MODE_; + +static void create_partition_arrays(); +static void init_partition_arrays(); +static void fill_partition_arrays(); +static void free_partition_arrays(); + +static void calc_u(int i, int j); +static void calc_ud(int i, int j); +static void calc_up(int i, int j); +static void calc_upm(int i, int j); +static void calc_u1(int i, int j); +static void calc_u1d(int i, int j); +static void calc_s1(int i, int j); +static void calc_s2(int i, int j); +static void calc_s3(int i, int j); + +static double get_u(int i, int j); +static double get_ud(int i, int j); +static double get_up(int i, int j); +static double get_upm(int i, int j); +static double get_u1(int i, int j); +static double get_u1d(int i, int j); +static double get_s1(int i, int j); +static double get_s2(int i, int j); +static double get_s3(int i, int j); + + +static void set_u(int i, int j, double val); +static void set_ud(int i, int j, double val); +static void set_up(int i, int j, double val); +static void set_upm(int i, int j, double val); +static void set_u1(int i, int j, double val); +static void set_u1d(int i, int j, double val); +static void set_s1(int i, int j, double val); +static void set_s2(int i, int j, double val); +static void set_s3(int i, int j, double val); + + +void errorAndExit(char* msg, int i, int j, double oldVal, double newVal){ + printf("%s", msg); + printf("i=%d,j=%d,oldVal=%0.1f,newVal=%0.1f\n",i,j,oldVal,newVal); + printf("%s","\nprogram is exiting now due to above error\n"); + exit(-1); +} + +double get_u(int i, int j) {if(u[i][j]==-1) errorAndExit("get_u entry is -1.",i,j,-1,0); return u[i][j];} +double get_ud(int i, int j) {if(ud[i][j]==-1) errorAndExit("get_ud entry is -1.\n",i,j,-1,0); return ud[i][j];} +double get_up(int i, int j) {if(up[i][j]==-1) errorAndExit("get_up entry is -1.\n",i,j,-1,0); return up[i][j];} +double get_upm(int i, int j) {if(upm[i][j]==-1) errorAndExit("get_upm entry is -1.\n",i,j,-1,0); return upm[i][j];} +double get_u1(int i, int j) {if(u1[i][j]==-1) errorAndExit("get_u1 entry is -1.\n",i,j,-1,0); return u1[i][j];} +double get_u1d(int i, int j) {if(u1d[i][j]==-1) errorAndExit("get_u1d entry is -1.\n",i,j,-1,0); return u1d[i][j];} +double get_s1(int i, int j) {if(s1[i][j]==-1) errorAndExit("get_s1 entry is -1.\n",i,j,-1,0); return s1[i][j];} +double get_s2(int i, int j) {if(s2[i][j]==-1) errorAndExit("get_s2 entry is -1.\n",i,j,-1,0); return s2[i][j];} +double get_s3(int i, int j) {if(s3[i][j]==-1) errorAndExit("get_s3 entry is -1.\n",i,j,-1,0); return s3[i][j];} + + +void set_u(int i, int j, double val) {if(u[i][j]!=-1 && u[i][j]!=val) errorAndExit("set_u entry is not -1.\n",i,j,u[i][j],val); u[i][j]=val;} +void set_ud(int i, int j, double val) {if(ud[i][j]!=-1 && ud[i][j]!=val) errorAndExit("set_ud entry is not -1.\n",i,j,ud[i][j],val); ud[i][j]=val;} +void set_up(int i, int j, double val) {if(up[i][j]!=-1 && up[i][j]!=val) errorAndExit("set_up entry is not -1.\n",i,j,up[i][j],val); up[i][j]=val;} +void set_upm(int i, int j, double val) {if(upm[i][j]!=-1 && upm[i][j]!=val) errorAndExit("set_upm entry is not -1.\n",i,j,upm[i][j],val); upm[i][j]=val;} +void set_u1(int i, int j, double val) {if(u1[i][j]!=-1 && u1[i][j]!=val) errorAndExit("set_u1 entry is not -1.\n",i,j,u1[i][j],val); u1[i][j]=val;} +void set_u1d(int i, int j, double val) {if(u1d[i][j]!=-1 && u1d[i][j]!=val) errorAndExit("set_u1d entry is not -1.\n",i,j,u1d[i][j],val); u1d[i][j]=val;} +void set_s1(int i, int j, double val) {if(s1[i][j]!=-1 && s1[i][j]!=val) errorAndExit("set_s1 entry is not -1.\n",i,j,s1[i][j],val); s1[i][j]=val;} +void set_s2(int i, int j, double val) {if(s2[i][j]!=-1 && s2[i][j]!=val) errorAndExit("set_s2 entry is not -1.\n",i,j,s2[i][j],val); s2[i][j]=val;} +void set_s3(int i, int j, double val) {if(s3[i][j]!=-1 && s3[i][j]!=val) errorAndExit("set_s3 entry is not -1.\n",i,j,s3[i][j],val); s3[i][j]=val;} + +double myExp(double arg){ + double posArgMultRT = (-1)*arg*RT; + if(posArgMultRT>=INFINITY_){ + //printf("WARN: posArgMultRT is greater than or equal to INFINITY_, hence returning zero\n"); + return 0; + } + return exp(arg); +} + +double eS_new(int i, int j){ + if(PF_COUNT_MODE_) return 0; + return eS(i,j); +} + +double eH_new(int i, int j){ + if(PF_COUNT_MODE_) return 0; + return eH(i,j); +} + +double eL_new(int i, int j, int p, int q){ + if(PF_COUNT_MODE_) return 0; + return eL(i,j,p,q); +} + +double ED3_new(int i, int j, int k){ + if(PF_COUNT_MODE_) return 0; + //if (j-i > TURN && canPair(RNA[i],RNA[j])) { + // assert(Ed5(j,i,k)<0.1); + //} + return Ed5(j,i,k); +} + +double ED5_new(int i, int j, int k){ + if(PF_COUNT_MODE_) return 0; + if (k<1) return 0; + + //if (j-i > TURN && canPair(RNA[i],RNA[j])) { + // assert(Ed3(j,i,k)<0.1); + //} + return Ed3(j,i,k); +} + +double EA_new(){ + if(PF_COUNT_MODE_) return 0; + return Ea; +} + +double EB_new(){ + if(PF_COUNT_MODE_) return 0; + return Ec; +} + +double EC_new(){ + if(PF_COUNT_MODE_) return 0; + return Eb; +} + +double auPenalty_new(int i, int j){ + if(PF_COUNT_MODE_) return 0; + return auPenalty(i,j); +} + +double f(int j, int h, int l){ + if(j - 1 == l) + return 1; + else + return myExp(-ED3_new(h,l,l+1)/RT); +} + +void printMatrix(double** u, int part_len){ + int i,j; + for (i = 0; i <= part_len+1; ++i) + { + for (j = 0; j <= part_len+1; ++j) + printf("%0.1f ",u[i][j]); + printf("\n"); + } +} + +void printAllMatrixes(){ + printf("\n\nAfter calculation, u matrix:\n\n"); + printMatrix(u,part_len); + printf("\n\nAfter calculation, ud matrix:\n\n"); + printMatrix(ud,part_len); + printf("\n\nAfter calculation, up matrix:\n\n"); + printMatrix(up,part_len); + printf("\n\nAfter calculation, upm matrix:\n\n"); + printMatrix(upm,part_len); +printf("\n\nAfter calculation, u1 matrix:\n\n"); + printMatrix(u1,part_len); +printf("\n\nAfter calculation, u1d matrix:\n\n"); + printMatrix(u1d,part_len); +printf("\n\nAfter calculation, s1 matrix:\n\n"); + printMatrix(s1,part_len); +printf("\n\nAfter calculation, s2 matrix:\n\n"); + printMatrix(s2,part_len); +printf("\n\nAfter calculation, s3 matrix:\n\n"); + printMatrix(s3,part_len); + +} + +double calculate_partition(int len, int pf_count_mode) +{printf("RT=%f\n",RT);//RT=RT/100; + PF_COUNT_MODE_ = pf_count_mode; + //int i, j; + part_len = len; + create_partition_arrays(); + init_partition_arrays(); + + /*printf("\nAfter initialization but before calculation, u matrix:\n\n"); + for (i = 0; i <= part_len+1; ++i) + { + for (j = 0; j <= part_len+1; ++j) + printf("%0.1f ",u[i][j]); + printf("\n"); + } + + printf("%4.4f\n",u[1][part_len]);*/ + + fill_partition_arrays(); + + //printAllMatrixes(); + + printf("%4.4f\n",u[1][part_len]); + + return u[1][part_len]; +} + +void free_partition() +{ + free_partition_arrays(); +} + +void init_part_arrays_zeros(){ + int i,j,n; + n = part_len+1; + for(i=0; i<=n; ++i){ + for(j=0; j<=n; ++j){ + u[i][j]=0; + up[i][j]=0; + upm[i][j]=0; + ud[i][j]=0; + u1d[i][j]=0; + + s1[i][j]=0; + s2[i][j]=0; + s3[i][j]=0; + u1[i][j]=0; + } + } +} + +void init_part_arrays_ones(){ + int i,j,n; + n = part_len+1; + for(i=0; i<=n; ++i){ + for(j=0; j<=n; ++j){ + u[i][j]=1; + up[i][j]=1; + upm[i][j]=1; + ud[i][j]=1; + u1d[i][j]=1; + + s1[i][j]=1; + s2[i][j]=1; + s3[i][j]=1; + u1[i][j]=1; + } + } +} + + +void init_part_arrays_negatives(){ + int i,j,n; + n = part_len+1; + for(i=0; i<=n; ++i){ + for(j=0; j<=n; ++j){ + u[i][j]=-1; + up[i][j]=-1; + upm[i][j]=-1; + ud[i][j]=-1; + u1d[i][j]=-1; + + s1[i][j]=-1; + s2[i][j]=-1; + s3[i][j]=-1; + u1[i][j]=-1; + } + } + for(i=0; i<=n+1; ++i){ + for(j=0; j<=n+1; ++j){ + u1[i][j]=-1; + } + } +} + +void init_partition_arrays() +{//ERROR_FOUND first nested for loop was wrongly written and iterated + //init_part_arrays_zeros(); + //init_part_arrays_ones(); + init_part_arrays_negatives(); + + int i, j; + int n = part_len; + for(i=1; i<=n; ++i){ + for(j=i; j<=i+TURN && j<=n; ++j){ //if(j>n)continue; + u[i][j] = 1; + up[i][j] = 0; + ud[i][j] = 0; + u1[i][j] = 0; + u1d[i][j] =0 ; + s1[i][j] = 0; + s2[i][j] = 0; + s3[i][j] = 0; + } + } + for(i=1; (i+TURN)<=n; ++i){ + //s1[i][i+TURN] = 0; + //s2[i][i+TURN] = 0; + } + + for(i=1; (i+TURN+1)<=n; ++i){//ERROR no need to do this as it will already be calculated as zero only + //s1[i][i+TURN+1] = 0; + //s2[i][i+TURN+1] = 0; + } + + /*for(i=1; i<=n-4; ++i){ + s1[i][i+4] = 0; + s2[i][i+4] = 0; + }*/ + for(i=1; i<=n; ++i){ + u[i+1][i] = 1; + u1[i+1][i] = 0; + u1d[i+1][i] = 0; + } + for(i=1; i<=n; i++){//for(i=1; i<=n-1; i++){ + u1[i+2][i] = 0; + } + +} + +/* +void init_partition_arrays() +{ + //init_part_arrays_zeros(); + init_part_arrays_negatives(); + + int i, j; + int n = part_len; + for(i=1; i<=n-3; ++i){ + for(j=i; j<=i+3; ++j){ + u[i][j] = 1; + up[i][j] = 0; + ud[i][j] = 0; + u1[i][j] = 0; + u1d[i][j] =0 ; + s1[i][j] = 0; + s2[i][j] = 0; + s3[i][j] = 0; + } + } + for(i=1; i<=n-4; ++i){ + s1[i][i+4] = 0; + s2[i][i+4] = 0; + } + for(i=1; i<=n; ++i){ + u[i+1][i] = 1; + u1[i+1][i] = 0; + u1d[i+1][i] = 0; + } + for(i=1; i<=n-1; i++){ + u1[i+2][i] = 0; + } +}*/ +/* +void fill_partition_arrays() +{ + int b,i,j; + int n=part_len; + for(b=TURN+1; b TURN) + { + for(l=i+2; l TURN) + { + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + + for (q = minq; q <= maxq; q++) { + if (canPair(p,q)==0) continue; + up_val += (up[p][q] * myExp(-eL_new(i,j,p,q)/RT)); + } + } + + up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); + up_val = up_val + myExp(-eH_new(i,j)/RT ); + up_val = up_val + myExp(-eS_new(i,j)/RT ) * up[i+1][j-1]; + up_val = up_val + upm[i][j]; + + up[i][j] = up_val; + } + else { + up[i][j] = 0; + } +}*/ + +void printUPprobabilities(int i, int j){ + int h,l; + double maxIntLoopProb = 0.0; + int h_max=-1, l_max=-1; + double sum=0.0; + for (h = i+1; h < j ; h++) { + for (l = h+1; l < j; l++) { + if (canPair(RNA[h],RNA[l])==0) continue; + if(h==(i+1) && l==(j-1)) continue; + //if((l-h)<=TURN) continue; + double intLoopProb = (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT))/up[i][j]; + sum+=intLoopProb; + if(intLoopProb > maxIntLoopProb){ maxIntLoopProb = intLoopProb; h_max=h; l_max=l;} + } + } + + //ERROR below line should not be there + //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); + double hpProb = myExp(-((double)eH_new(i,j))/RT )/up[i][j]; + double stackProb = (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1))/up[i][j]; + double upmProb = get_upm(i,j)/up[i][j]; + + if(maxIntLoopProb>=hpProb && maxIntLoopProb>=stackProb && maxIntLoopProb >=upmProb) printf("INT "); + else if(hpProb>=maxIntLoopProb && hpProb>=stackProb && hpProb>=upmProb) printf("HPL "); + else if(stackProb>=hpProb && stackProb>=maxIntLoopProb && stackProb>=upmProb) printf("STK "); + else if(upmProb>=hpProb && upmProb>=stackProb && upmProb>=maxIntLoopProb) printf("UPM "); + + printf("printing probabilities: i=%d, j =%d, upmProb=%.6f, stackProb=%.6f, hpProb=%.6f, maxIntLoopProb=%.6f, sumIntLoopProbs=%.6f, h_max=%d, l_max=%d\n",i,j, upmProb, stackProb, hpProb, maxIntLoopProb,sum,h_max,l_max); + +} + +void calc_up(int i, int j) +{//printf("Entering calc_up: i=%d, j =%d\n",i,j); + double up_val = 0.0; + //int p,q; + + if (canPair(RNA[i],RNA[j]))// if(j-i>TURN) + { + int h,l; + for (h = i+1; h < j ; h++) { + for (l = h+1; l < j; l++) { + if (canPair(RNA[h],RNA[l])==0) continue; + if(h==(i+1) && l==(j-1)) continue; + up_val += (get_up(h,l) * myExp(-((double)eL_new(i,j,h,l))/RT)); + } + } + + //ERROR below line should not be there + //up_val = up_val * myExp(-ED3_new(i,j,i+1)/RT); + up_val = up_val + myExp(-((double)eH_new(i,j))/RT ); + up_val = up_val + (myExp(-((double)eS_new(i,j))/RT ) * get_up(i+1,j-1)); + up_val = up_val + get_upm(i,j); + + set_up(i, j, up_val);//up[i][j] = up_val; + + } + else { + set_up(i, j, 0.0);//up[i][j] = 0; + } +} diff --git a/gtfold-mfe/src/random-sample.cc b/gtfold-mfe/src/random-sample.cc new file mode 100644 index 0000000..c336b68 --- /dev/null +++ b/gtfold-mfe/src/random-sample.cc @@ -0,0 +1,559 @@ +#include +#include +#include + +#include "partition-dangle.h" +#include "algorithms-partition.h" +#include "energy.h" +#include "random-sample.h" + +using namespace std; + +#define MIN_TURN 4 + +//double RT=(0.00198721 * 310.15)/100.00; + + +//I don't know why not having this function +//gives me a link error it should get this function +//from partition-dangle + +/*double cond_dangle(int j, int h, int l){ + if(j - 1 == l) + return 1; + else + return exp(-Ed3(h,l,l+1)/RT); +}*/ + +double randdouble(){ + return rand()/(double(RAND_MAX)+1); +} + +//P_0 +double single_stranded_prob(int i, int j, dangle_struct d_struct){ + return 1 / d_struct.u[i][j]; +} + +//P_{ij} +double ends_pair_prob(int i, int j, dangle_struct d_struct){ + return d_struct.up[i][j] * exp(-auPenalty(i,j)/RT)/d_struct.u[i][j]; +} + +//P_{hj} +double prob_h_pairs_with_5_end + (int i, int h, int j, dangle_struct d_struct){ + + return d_struct.up[h][j] * + exp(-(Ed5(h,j,h - 1) + + auPenalty(h,j))/RT) / + d_struct.u[i][j]; +} + +//P_{il} +double prob_l_pairs_with_3_end + (int i, int l, int j, dangle_struct d_struct){ + + return d_struct.up[i][l] * exp(-auPenalty(i,l)/RT) * + (exp(-Ed3(i,l,l+1)/RT) * d_struct.u[l + 2][j] + + d_struct.u[l + 1][j] - + d_struct.u[l + 2][j]) / + d_struct.u[i][j]; +} + +//P_{s1h} +double prob_h_pairs_in_ij(int i, int h, int j, dangle_struct d_struct){ + return d_struct.s1[h][j] / d_struct.u[i][j]; +} + +//P_{hl} +//This is the probability h pairs with l +//**Given that h pairs before j** +double prob_h_pairs_with_l(int h, int l, int j, dangle_struct d_struct){ + return d_struct.up[h][l] * exp(-(Ed5(h,l,h - 1) + auPenalty(h,l))/RT) * + (exp(-Ed3(h,l,l + 1)/RT) * d_struct.u[l + 2][j] + + d_struct.u[l + 1][j] - + d_struct.u[l + 2][j]) / + d_struct.s1[h][j]; +} + +//Q_{ijH} +double prob_ij_pair_is_hairpin(int i, int j, dangle_struct d_struct){ + return exp(-eH(i,j)/RT)/d_struct.up[i][j]; +} + +//Q_{ijS} +double prob_ij_pair_is_stack(int i, int j, dangle_struct d_struct){ + return exp(-eS(i,j)/RT) * d_struct.up[i + 1][j - 1]/d_struct.u[i][j]; +} +//To find Q_{ijBl} take the rest of the probabilities and subtract +//them from 1. + +//Q_{ijM} +double prob_ij_pair_is_multiloop(int i, int j, dangle_struct d_struct){ + return d_struct.upm[i][j]/d_struct.up[i][j]; +} + +//This the probability hl closes a multiloop +//**GIVEN IJ CLOSES A MULTILOOP** +double prob_ijhl_is_internal_loop + (int i, int j, int h, int l, double partition_sum, dangle_struct d_struct){ + return exp(-eL(i,j,h,l)/RT) * d_struct.up[h][l] / partition_sum; +} + +//P_{ij(1+1)l} +double first_multi_prob_pair_next_base + (int i, int l, int j, dangle_struct d_struct){ + return d_struct.up[i + 1][l] * + (exp( - (Ea + 2 * Ec + auPenalty(i + 1, l))/RT) * + (exp(-Ed3(i + 1,l,l +1))/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 1][j - 1]) / + d_struct.upm[i][j]; +} + +//P_{ij(1+2)l} +double first_multi_prob_pair_after_base + (int i, int l, int j, dangle_struct d_struct){ + + return d_struct.up[i + 2][l] * + exp(-(Ea + 2 * Ec + Eb + Ed3(j, i, i + 1) + auPenalty(i + 2,l))/RT) * + (exp(-Ed3(i + 2,l,l+1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1]) / + d_struct.upm[i][j]; +} + +//P_{ijs2h) +double first_multi_prob_pair_rest_base(int i, int h, int j, dangle_struct d_struct){ + return exp(-(Ea + 2 * Ec + (h - i - 1) * Eb + Ed3(j,i,i+1))/RT) * + d_struct.s2[h][j] / d_struct.upm[i][j]; +} +//P_{ijhl} +double first_multi_prob_base_rest + (int i, int h, int l, int j, dangle_struct d_struct){ + + return d_struct.up[h][l] * exp(-(Ed5(h,l,h-1) + auPenalty(h,l))/RT) * + (exp( -Ed3(h,l,l+1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1])/d_struct.s2[h][j]; +} + +//Q_{(l1 + 1)(j -1)(l1 +1)} +double rest_multi_prob_next_base_pairs (int l1, int l, int j, dangle_struct d_struct){ + + return d_struct.up[l1 +1][l] * exp(-(Ec + auPenalty(l1 + 1, l))/RT) * + (cond_dangle(j, l1 + 1, l) * exp( -(j - 1 - l) * Eb /RT) + + exp(-(j - 1 - l) * Eb) / RT + + exp(-Ed3(l1 + 1, l, l + 1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 1][j - 1]) / + d_struct.u1[l1 + 1][j - 1]; +} + +//Q_{(l1 + 1)(j - 1)(l1 + 2)l} +double rest_multi_prob_after_base_pairs + (int l1, int l, int j, dangle_struct d_struct){ + + return d_struct.up[l1 + 2][l] * exp(-(Ec + Eb + auPenalty(l1 + 2,l))/RT) * + (cond_dangle(j, l1 + 2, l) * exp( -(j - 1 - l) * Eb / RT) + + exp(-Ed3(l1 + 1,l ,l + 1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1]) / + d_struct.u1[l1 + 1][j - 1]; + +} + +//Q_{(l1 + 1)(j - 1)s3h} +double rest_multi_prob_rest_base_pairs + (int l1, int h, int j, dangle_struct d_struct){ + + return exp( -(Ec + (h - l1 - 1) * Eb)/RT) * d_struct.s3[h][j - 1] / + d_struct.u1[l1 + 1][j - 1]; +} + +//Q_{(j-1)hl} +//GIVEN THAT H PAIRS BEFORE J +double rest_multi_prob_h_pairs_with_l + (int l1, int h, int l, int j, dangle_struct d_struct){ + + return d_struct.up[h][l] * exp(-(Ed5(h,l,h - 1) + auPenalty(h,l))/RT) * + (cond_dangle(j,h,l) * exp(-(j - 1 -l) * Eb/RT) + + exp(-Ed3(h,l,l + 1)/RT) * d_struct.u1[l + 2][j - 1] + + d_struct.u1[l + 1][j - 1] - + d_struct.u1[l + 2][j - 1]) / + d_struct.s3[h][j - 1]; +} + +//P_{Bh2l2} +int there_is_another_helix(int h2, int l2, int j, dangle_struct d_struct){ + double counter = randdouble(); + double coin_flip = cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) / + (cond_dangle(j,h2,l2) * exp(-(j - 1 - l2) * Eb / RT) + + exp(Ed3(h2,l2,l2 + 1)/RT) * d_struct.u1[l2 + 2][j - 1] + + d_struct.u1[l2 + 1][j - 1] - + d_struct.u1[l2 + 2][j - 1]); + + //If I was slick and mean I would have put + + //return counter > coin-flip + + if(counter <= coin_flip){ + return 0; + } + else{ + return 1; + } +} + +void single_stranded(int i, int j, int * structure){ + for(;i <= j; i++) + { + structure[i] = 0; + } +} + +void unknown_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack){ +//Unknown strand from i,j + double counter = randdouble(); + counter -= single_stranded_prob(i, j, d_struct); + if (counter <= 0){ + single_stranded(i,j, structure); + return; + } + counter -= ends_pair_prob(i, j, d_struct); + if(counter <= 0){ + sub_seq seq; + seq.start = i; + seq.end = j; + seq.paired = 1; + //put i j on paired and push i j on stack as paired + + structure[i] = j; + structure[j] = i; + stack->push_front(seq); + return; + } + for (int h = i + MIN_TURN; h < j; h++){ + counter -= prob_h_pairs_with_5_end(i,h,j,d_struct); + if(counter < 0){ + sub_seq seq1; + sub_seq seq2; + + seq1.start = i; + seq1.end = h; + seq1.paired = 1; + + seq2.start = h + 1; + seq2.end = j; + seq2.paired = 0; + + //Push i h as paired and h + 1 to j as unknown + structure[i] = h; + structure[h] = i; + stack->push_front(seq1); + stack->push_front(seq2); + return; + } + } + + for(int l = i + 1; l <= j - MIN_TURN; l++){ + counter -= prob_l_pairs_with_3_end(i,l,j,d_struct); + if (counter < 0){ + + sub_seq seq; + seq.start = l; + seq.end = j; + seq.paired = 1; + + //put from i to l - 1 as unpaired and push l and j as paired + single_stranded(i, l - 1, structure); + structure[l] = j; + structure[j] = l; + stack->push_front(seq); + return; + } + } + int h; //The loop is just to find h we need it later + for(h = i + 1; i <= j - MIN_TURN - 1; h++){ + counter -= prob_h_pairs_in_ij(i,h,j,d_struct); + if(counter < 0) + { + break; + } + } + + //Now to find l + counter = randdouble(); //reset counter, this is a seperate case + for(int l = h + MIN_TURN; l <= j - MIN_TURN; l++){ + counter -= prob_h_pairs_with_l(h,l,j,d_struct); + if (counter < 0){ + sub_seq seq1; + sub_seq seq2; + + seq1.start = h; + seq1.end = l; + seq1.paired = 1; + + seq2.start = l + 1; + seq2.end = j; + seq2.paired = 0; + + //set from i to h - 1 as single stranded + //Push h l as paired and l + 1 to j + //as unknown. + + single_stranded(i, h - 1, structure); + structure[h] = l; + structure[l] = h; + stack->push_front(seq1); + stack->push_front(seq2); + return; + } + } + //If we hit here, that's bad +} + +void paired_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack){ + double counter = randdouble(); + double cumulative_prob = 0; + + + cumulative_prob = prob_ij_pair_is_hairpin(i,j,d_struct); + if(counter - cumulative_prob < 0){ + //i + 1, j - 1 is single stranded + single_stranded(i + 1, j - 1, structure); + return; + } + + cumulative_prob += prob_ij_pair_is_stack(i,j,d_struct); + if(counter - cumulative_prob < 0){ + sub_seq seq; + seq.start = i + 1; + seq.end = j - 1; + seq.paired = 1; + + //i + 1, j - 1 is pushed as stack + stack->push_front(seq); + structure[i + 1] = j - 1; + structure[j - 1] = i + 1; + return; + } + + cumulative_prob += prob_ij_pair_is_multiloop(i,j,d_struct); + if(counter - cumulative_prob < 0){ + multi_loop_strand(i,j,d_struct,structure,stack); + return; + } + + //else we know we have an internal loop. + //The probabilities should work out so that + //we never get more than 30 base internal loops. + //Might need to put guards in here. + counter = randdouble(); + for(int h = i + 1; h < j; h++){ + for(int l = h + MIN_TURN; l < j; l++){ + if(!(h == i + 1 && l == j - 1)) //Don't want a stack + counter -= exp(-eL(i,j,h,l)/RT) * d_struct.up[h][l] / (1 - cumulative_prob); + if(counter < 0){ + sub_seq seq; + seq.start = h; + seq.end = l; + seq.paired = 1; + + //hl goes on the stack as a pair and the rest of the internal loop + //gets put on a single stranded + + stack->push_front(seq); + structure[h] = l; + structure[l] = h; + single_stranded(i + 1, h - 1,structure); + single_stranded(l + 1, j - 1,structure); + } + } + } +} + +//It returns where it stops. +int multi_first_loop(int i, int j, dangle_struct d_struct, int * structure, list * stack){ + double counter = randdouble(); + for(int l= i + MIN_TURN + 1; l < j - 1; l++){ + counter -= first_multi_prob_pair_next_base(i,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = i + 1; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 1 pairs with l; + + stack->push_front(seq); + structure[i + 1] = l; + structure[l] = i + 1; + return l + 1; + } + } + for(int l = i + MIN_TURN + 2; l < j - 1; l++){ + counter -= first_multi_prob_pair_after_base(i,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = i + 2; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 2 pairs with l; + //and i + 1 is unpaired + + stack->push_front(seq); + structure[i + 1] = 0; + structure[i + 2] = l; + structure[l] = i + 2; + return l + 1; + } + } + + //We need h after this loop so we declare it here. + int h; + for(h = i + 3; h < j - 1; h ++){ + counter -= first_multi_prob_pair_rest_base(i,h,j,d_struct); + if(counter < 0){ + break; + } + } + + //Now h is the opening base in a base pair now we need to find the closing one + //So first we start a new counter + counter = randdouble(); + for (int l = h + MIN_TURN; l < j - 1; l++){ + counter -= first_multi_prob_base_rest(i,h,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = h; + seq.end = l; + seq.paired = 1; + + //H pairs with l and i + 1 to h - 1 is single stranded + single_stranded(i + 1, h - 1, structure); + stack->push_front(seq); + structure[h] = l; + structure[l] = h; + return l + 1; + } + } + + return -1; //We have an underflow or calculation error. +} + +void multi_loop_strand(int i, int j, dangle_struct d_struct, int * structure, list * stack){ + int l1 = multi_first_loop(i,j,d_struct, structure,stack);//l1 is the name of the closing base of the first loop + int h1 = i; + int notdone = 1; + int breakflag = 0; + + while(notdone){ + double counter = randdouble(); + for(int l = l1 + MIN_TURN + 1; l < j - 1; l++){ + counter -= rest_multi_prob_next_base_pairs(l1,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = l1 + 1; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 1 pairs with l; + + stack->push_front(seq); + structure[l1 + 1] = l; + structure[l] = i + 1; + h1 = l1 + 1; + l1 = l; + breakflag = 1; + break; + } + } + if(breakflag){ + notdone = there_is_another_helix(h1, l1, j, d_struct); + breakflag = 0; + continue; //Starts while loop over + } + for(int l = l1 + MIN_TURN + 2; l < j - 1; l++){ + counter -= rest_multi_prob_after_base_pairs(l1,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = l1 + 2; + seq.end = l; + seq.paired = 1; + + //Under this condition i + 2 pairs with l; + //and i + 1 is unpaired + + stack->push_front(seq); + structure[l1 + 1] = 0; + structure[l1 + 2] = l; + structure[l] = l1 + 2; + h1 = l1 + 2; + l1 = l; + breakflag = 1; + break; + } + } + if(breakflag){ + notdone = there_is_another_helix(h1, l1, j, d_struct); + breakflag = 0; + continue; //Starts while loop over + } + //We need h after this loop so we declare it here. + int h; + for(h = l1 + 3; h < j - 1; h ++){ + counter -= rest_multi_prob_rest_base_pairs(i,h,j,d_struct); + if(counter < 0){ + break; + } + } + + //Now h is the opening base in a base pair now we need to find the closing one + //So first we start a new counter + counter = randdouble(); + for (int l = h + MIN_TURN; l < j - 1; l++){ + counter -= rest_multi_prob_h_pairs_with_l(l1,h,l,j,d_struct); + if(counter < 0){ + sub_seq seq; + seq.start = h; + seq.end = l; + seq.paired = 1; + + //H pairs with l and i + 1 to h - 1 is single stranded + single_stranded(l1 + 1, h - 1, structure); + stack->push_front(seq); + structure[h] = l; + structure[l] = h; + l1 = l + 1; + h1 = h; + } + } + notdone = there_is_another_helix(h1, l1, j, d_struct); + }//End while +}//End function + + +void sample_structure(int * structure, dangle_struct d_struct){ + sub_seq seq; + seq.start = 1; + seq.end = d_struct.length; + seq.paired = 0; + + list da_stack; + da_stack.push_front(seq); + while(!da_stack.empty()){ + sub_seq cur_seq = da_stack.front(); + if(cur_seq.paired) + { + paired_strand(cur_seq.start, cur_seq.end, d_struct, structure, &da_stack); + } + else + { + unknown_strand(cur_seq.start, cur_seq.end, d_struct, structure, &da_stack); + } + da_stack.pop_front(); + } + +} diff --git a/gtfold-mfe/src/shapereader.cc b/gtfold-mfe/src/shapereader.cc new file mode 100644 index 0000000..006f8a1 --- /dev/null +++ b/gtfold-mfe/src/shapereader.cc @@ -0,0 +1,95 @@ +#include +#include +#include +#include +#include +#include + +#include "shapereader.h" +#include "global.h" +#include "options.h" + +using namespace std; + +double* SHAPEarray; +int* SHAPEenergies; + +static bool SHAPE_ENABLED = false; + +void enable_shape(bool b) { + SHAPE_ENABLED = b; +} + +void free_shapeArray(int len){ + free(SHAPEarray); +} + +void print_shapeArray(int len){ + for(int i=0; i0){ + if(sscanf(line.c_str(), "%d %lf", &position, &SHAPEnumber)==2){ + if(position <= seqlength){ + SHAPEarray[position] = SHAPEnumber; + SHAPEenergies[position] = calcShapeEnergy(SHAPEnumber); + } + else{ + printf("Invalid SHAPE position indicator (ignoring line): %s\n", line.c_str()); + } + }else{ + printf("Invalid line (ignoring): %s\n", line.c_str()); + } + } + +} + +int getShapeEnergy(int position){ + if(SHAPE_ENABLED){ + return SHAPEenergies[position]; + } + else{ + return 0; + } +} + +int calcShapeEnergy(double shapeNumber){ +//ZS: This function returns the free energy contribution as an integer. + if(shapeNumber<(double)0){ + return 0; + } + else{ + double energy = shapeModel(shapeNumber); + return (int)floor(100.0*energy+ .5); + } +} + + +double shapeModel(double SHAPE_value){ +//ZS: This function calculates the free energy contribution due to SHAPE. + double m = 2.6; + double b = -0.8; + return m*log(SHAPE_value+1)+b; +} + + + + diff --git a/gtfold-mfe/src/stochastic-sampling.cc b/gtfold-mfe/src/stochastic-sampling.cc new file mode 100644 index 0000000..b831ff8 --- /dev/null +++ b/gtfold-mfe/src/stochastic-sampling.cc @@ -0,0 +1,759 @@ +#include "stochastic-sampling.h" + +#include "global.h" +#include +#include +#include +#include +#include +#include + +int ss_verbose = 0; + +std::stack g_stack; + +double energy = 0; + +double randdouble() +{ + return rand()/(double(RAND_MAX)+1); +} + +bool feasible(int i, int j) +{ + return j-i > TURN && canPair(RNA[i],RNA[j]); +} + +double U_0(int i, int j) +{ + return 1.0/u[i][j]; +} + +double U_ij(int i, int j) +{ + return (feasible(i,j) == true)?up[i][j]*exp(-auPenalty_new(i,j)/RT)/u[i][j]:0; +} + +double U_hj(int i, int h, int j) +{ + return (feasible(h,j) == true)?up[h][j]*exp(-(ED5_new(h,j,h-1)+auPenalty_new(h,j))/RT)/u[i][j]:0; +} + +double U_il(int i, int j) +{ + return ud[i][j]/u[i][j]; +} + +double U_s1h(int i, int h, int j) +{ + return s1[h][j]/u[i][j]; +} + +double U_ihlj_case1(int i, int h, int l, int j) +{ + return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (exp(-ED3_new(h,l,l+1)/RT)*u[l+2][j]) /s1[h][j]:0; +} + +double U_ihlj_case2(int i, int h, int l, int j) +{ + return feasible(h,l)?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (ud[l+1][j]) /s1[h][j]:0; +} + +double U_ihlj_case3(int i, int h, int l, int j) +{ + return (feasible(h,l)&&feasible(l+1,j))?up[h][l]*exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT)* (up[l+1][j]*exp(-(auPenalty_new(l+1,j)/RT))) /s1[h][j]:0; +} + +double UD_il_case1(int i, int l, int j) +{ + return feasible(i,l)?(up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*exp(-1*ED3_new(i,l,l+1)/RT)*u[l+2][j])/ud[i][j]:0; +} + +double UD_il_case2(int i, int l, int j) +{ + return feasible(i,l)?(up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*ud[l+1][j])/ud[i][j]:0; +} + +double UD_il_case3(int i, int l, int j) +{ + return (feasible(i,l)&&feasible(l+1,j))?up[i][l]*exp(-1*auPenalty_new(i,l)/RT)*up[l+1][j]*exp(-1*auPenalty_new(l+1,j))/ud[i][j]:0; +} + +double Q_ijH(int i, int j) +{ + return exp(-eH_new(i,j)/RT)/up[i][j]; +} + +double Q_ijS(int i, int j) +{ + return exp(-eS_new(i,j)/RT)*up[i+1][j-1]/up[i][j]; +} + +double Q_ijM(int i, int j) +{ + return upm[i][j]/up[i][j]; +} + +/* +double Q_ijBI(int i, int j) +{ + double sum = 0; + for (int h = i+1; h < j-1; ++h) + for (int l = h+1; l < j; ++l) + { + if (h == i+1 && l == j-1) continue; + sum += feasible(h,l)?(exp(-1*eL_new(i,j,h,l)/RT)*up[h][l]):0; + } + return sum/up[i][j]; +}*/ + +double Q_ijhlBI(int i, int j, int h, int l) +{ + return feasible(h,l)?exp(-1*eL_new(i,j,h,l)/RT)*up[h][l]/up[i][j]:0; +} + +double UPM_ip1l_case1(int i, int l, int j) +{ + return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(EA_new()+2*EC_new()+auPenalty_new(i+1,l))/RT) * exp(-1*(ED3_new(i+1,l,l+1)+EB_new())/RT) * u1[l+2][j-1])/upm[i][j]:0; +} + +double UPM_ip1l_case2(int i, int l, int j) +{ + return feasible(i+1,l)?(up[i+1][l] * exp((-1)*(EA_new()+2*EC_new()+auPenalty_new(i+1,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; +} + +double UPM_ip2l_case1(int i, int l , int j) +{ + return feasible(i+2,l)?up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/RT) * (exp((-1)*(ED3_new(i+2,l,l+1)+EB_new())/RT)*u1[l+2][j-1])/upm[i][j]:0; +} + +double UPM_ip2l_case2(int i, int l , int j) +{ + return feasible(i+2,l)?(up[i+2][l]*exp((-1)*(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/RT) * u1d[l+1][j-1])/upm[i][j]:0; +} + + +double UPM_ijs2h(int i, int h , int j) +{ + return exp((-1)*ED3_new(j,i,i+1)/RT)* (s2[h][j] * exp((-1)*(EA_new()+2*EC_new()+(h-i-1)*EB_new())/RT))/upm[i][j]; +} + + +double UPM_ijhl_case1(int i, int h, int l, int j) +{ + return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (exp(-ED3_new(h,l,l+1)/RT)*u1[l+2][j-1])/s2[h][j]:0; +} + +double UPM_ijhl_case2(int i, int h, int l, int j) +{ + return feasible(h,l)?up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (u1d[l+1][j-1])/s2[h][j]:0; +} + +// u1d : case 1 +double U1D_ij_il_case1(int i, int l, int j) +{ + return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT) * (f(j+1,i,l)*exp((-1)*(j-l)*EB_new()/RT)))/u1d[i][j]:0; +} + +// u1d : case 2 +double U1D_ij_il_case2(int i, int l, int j) +{ + return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT)*(exp((-1)*(ED3_new(i,l,l+1)+EB_new())/RT)*u1[l+2][j]))/u1d[i][j]:0; +} + +// u1d : case 3 +double U1D_ij_il_case3(int i, int l, int j) +{ + return feasible(i,l)?(up[i][l]*exp((-1)*(EC_new()+auPenalty_new(i,l))/RT) * u1d[l+1][j])/u1d[i][j]:0; +} + +// u1 +double U1_ij(int i, int j) +{ + return u1d[i][j]/u1[i][j]; +} + +// u1 : sample h +double U1_ij_s3h(int i, int h, int j) +{ + return (s3[h][j] * exp((-1)*(EC_new()+(h-i)*EB_new())/RT))/u1[i][j]; +} + +// u1 : sample l +double U1_j_hl_case1(int h, int l, int j) +{ + return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (f(j+1,h,l)*exp(-((j-l)*EB_new())/RT))) /s3[h][j]:0; +} + +double U1_j_hl_case2(int h, int l, int j) +{ + return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (exp(-(ED3_new(h,l,l+1)+EB_new())/RT)*u1[l+2][j])) /s3[h][j]:0; +} + +double U1_j_hl_case3(int h, int l, int j) +{ + return feasible(h,l)?(up[h][l]*(exp(-(ED5_new(h,l,h-1)+auPenalty_new(h,l))/RT))* (u1d[l+1][j])) /s3[h][j]:0; +} + +void rnd_u(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0.0; + + + cum_prob += U_0(i,j); + if (rnd < cum_prob) + { + return; + } + + cum_prob += U_ij(i, j); + if (rnd < cum_prob) + { + energy += auPenalty_new(i,j); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,auPenalty_new(i,j)/100.0); + base_pair bp(i,j,UP); + g_stack.push(bp); + return; + } + + for (int h = i+1; h < j; ++h) + { + cum_prob += U_hj(i,h,j); + if (rnd < cum_prob) + { + energy += ED5_new(h,j,h-1)+auPenalty_new(h,j); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,(ED5_new(h,j,h-1)+auPenalty_new(h,j)) /100.0); + base_pair bp(h,j,UP); + //set_single_stranded(i,h-1,structure); + g_stack.push(bp); + return; + } + } + + cum_prob += U_il(i,j); + if (rnd < cum_prob) + { + base_pair bp1(i,j,UD); + g_stack.push(bp1); + return; + } + + int h1 = -1; + for (int h = i+1; h < j-1; ++h) + { + cum_prob += U_s1h(i,h,j); + if (rnd < cum_prob) + { + h1 = h; + break; + } + } + + assert (h1 != -1) ; + + rnd = randdouble(); + cum_prob = 0; + for (int l = h1+1; l < j; ++l) + { + cum_prob += U_ihlj_case1(i,h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+ auPenalty_new(h1,l) + ED3_new(h1,l,l+1)) /100.0); + base_pair bp1(h1,l,UP); + base_pair bp2(l+2,j,U); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + + cum_prob += U_ihlj_case2(i,h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); + + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j,UD); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + + cum_prob += U_ihlj_case3(i,h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + auPenalty_new(l+1,j)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + auPenalty_new(l+1,j))/100.0); + //set_single_stranded(i,h1-1,structure); + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j,UP); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + + } + assert(0); +} + +void rnd_ud(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0.0; + for (int l = i+1; l < j ; ++l) + { + cum_prob += UD_il_case1(i,l,j); + if (rnd < cum_prob) + { + energy += (auPenalty_new(i,l) + ED3_new(i,l,l+1)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l) + ED3_new(i,l,l+1))/100.0); + base_pair bp1(i,l,UP); + base_pair bp2(l+2,j,U); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += UD_il_case2(i,l,j); + if (rnd < cum_prob) + { + energy += auPenalty_new(i,l); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l))/100.0); + base_pair bp1(i,l,UP); + base_pair bp2(l+1,j,UD); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += UD_il_case3(i,l,j); + if (rnd < cum_prob) + { + energy += (auPenalty_new(i,l) + auPenalty_new(l+1,j)); + if (ss_verbose == 1) + printf("(%d %d) %lf\n",i,j, (auPenalty_new(i,l) + auPenalty_new(l+1,j))/100.0); + base_pair bp1(i,l,UP); + base_pair bp2(l+1,j,UP); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } + assert(0); +} + +void rnd_up(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + assert(structure[i] == 0); + assert(structure[j] == 0); + + set_base_pair(i,j,structure); + + cum_prob += Q_ijH(i,j); + if (rnd < cum_prob) + { + energy += eH_new(i,j); + if (ss_verbose == 1) + printf("Hairpin(%d %d) %lf\n",i,j, (eH_new(i,j))/100.0); + //set_single_stranded(i+1,j-1,structure); + return ; + } + + cum_prob += Q_ijS(i,j); + if (rnd < cum_prob) + { + energy += eS_new(i,j); + if (ss_verbose == 1) + printf("Stack(%d %d) %lf\n",i,j, (eS_new(i,j))/100.0); + base_pair bp(i+1,j-1,UP); + g_stack.push(bp); + return ; + } + + cum_prob += Q_ijM(i,j); + if (rnd < cum_prob) + { + rnd_upm(i,j,structure); + return; + } + + for (int h = i+1; h < j-1; ++h) + for (int l = h+1; l < j; ++l) + { + if (h == i+1 && l == j-1) continue; + cum_prob += Q_ijhlBI(i,j,h,l); + if (rnd < cum_prob) + { + energy += eL_new(i,j,h,l); + if (ss_verbose == 1) + printf("IntLoop(%d %d) %lf\n",i,j, (eL_new(i,j,h,l))/100.0); + base_pair bp(h,l,UP); + g_stack.push(bp); + return; + } + } + + assert(0); +} + +void rnd_u1(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + + cum_prob += U1_ij(i,j); + if (rnd < cum_prob) + { + base_pair bp(i,j,U1D); + g_stack.push(bp); + return; + } + + int h1 = -1; + for (int h = i+1; h < j-1; ++h) + { + cum_prob += U1_ij_s3h(i,h,j); + if (rnd < cum_prob) + { + energy += (EC_new()+(h-i)*EB_new()); + if (ss_verbose == 1) + printf("U1_ij_s3h(%d) %lf\n",h, (EC_new()+(h-i)*EB_new())/100.0); + h1 = h; + break; + } + } + + assert(h1 != -1); + // sample l given h1 + rnd = randdouble(); + cum_prob = 0; + for (int l = h1+1; l <= j ; ++l) + { + cum_prob += U1_j_hl_case1(h1,l,j); + if (rnd < cum_prob) + { + int tt = (j == l)?0:ED3_new(h1,l,l+1); + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new()); + if (ss_verbose == 1) + printf("U1_j_hl_case1(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + tt + (j-l)*EB_new())/100.0); + base_pair bp(h1,l,UP); + g_stack.push(bp); + return; + } + + cum_prob += U1_j_hl_case2(h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new()); + if (ss_verbose == 1) + printf("U1_j_hl_case2(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)+ ED3_new(h1,l,l+1)+EB_new())/100.0); + base_pair bp1(h1,l,UP); + base_pair bp2(l+2,j,U1); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += U1_j_hl_case3(h1,l,j); + if (rnd < cum_prob) + { + energy += ED5_new(h1,l,h1-1)+auPenalty_new(h1,l); + if (ss_verbose == 1) + printf("U1_j_hl_case3(%d %d) %lf\n",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } + + assert(0); +} + +void rnd_u1d(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + + for (int l = i+1; l <= j; ++l) + { + cum_prob += U1D_ij_il_case1(i,l,j); + if (rnd < cum_prob) + { + int tt = (j==l)?(0):(ED3_new(i,l,l+1)); + energy += ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new()); + if (ss_verbose == 1) { + printf("U1D_ij_il_case1(%d %d %d) %lf\n",i,l,j, ( EC_new()+auPenalty_new(i,l) + tt + (j-l)*EB_new())/100.0); + } + base_pair bp1(i,l,UP); + g_stack.push(bp1); + return; + } + + cum_prob += U1D_ij_il_case2(i,l,j); + if (rnd < cum_prob) + { + energy += (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new()); + if (ss_verbose == 1) + printf("U1D_ij_il_case2(%d %d) %lf\n",i,l, (EC_new()+auPenalty_new(i,l)+ ED3_new(i,l,l+1)+EB_new())/100.0); + base_pair bp1(i,l,UP); + base_pair bp2(l+2,j,U1); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += U1D_ij_il_case3(i,l,j); + if (rnd < cum_prob) + { + energy += (EC_new()+auPenalty_new(i,l)); + if (ss_verbose == 1) + printf("U1D_ij_il_case3(%d %d) %lf\n",i,l, (EC_new()+auPenalty_new(i,l))/100.0); + base_pair bp1(i,l,UP); + base_pair bp2(l+1,j,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } + assert(0); +} + +void rnd_upm(int i, int j, int* structure) +{ + double rnd = randdouble(); + double cum_prob = 0; + if (ss_verbose == 1) + printf("Multiloop (%d %d)\n",i,j); + + for (int l = i+2; l < j; ++l) + { + cum_prob += UPM_ip1l_case1(i,l,j); + if (rnd < cum_prob) + { + energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new()) ; + if (ss_verbose == 1) { + printf("(%d %d) %s %lf\n",i,j, "UPM_ip1l_case1",(EA_new()+2*EC_new()+auPenalty_new(i+1,l) + ED3_new(i+1,l,l+1)+EB_new())/100.0); + } + base_pair bp1(i+1,l,UP); + base_pair bp2(l+2,j-1,U1); + g_stack.push(bp2); + g_stack.push(bp1); + return ; + } + + cum_prob += UPM_ip1l_case2(i,l,j); + if (rnd < cum_prob) + { + energy += (EA_new()+2*EC_new()+auPenalty_new(i+1,l)); + if (ss_verbose == 1) + printf("(%d %d) %s %lf\n",i,j,"UPM_ip1l_case2", (EA_new()+2*EC_new()+auPenalty_new(i+1,l))/100.0); + base_pair bp1(i+1,l,UP); + base_pair bp2(l+1,j-1,U1D); + g_stack.push(bp2); + g_stack.push(bp1); + return ; + } + } + + for (int l = i+3; l < j; ++l) + { + cum_prob += UPM_ip2l_case1(i,l,j); + if (rnd < cum_prob) + { + energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new()); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n", "UPM_ip2l_case1", i,j,(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)+ED3_new(i+2,l,l+1)+EB_new())/100.0); + base_pair bp1(i+2,l,UP); + base_pair bp2(l+2,j-1,U1); + g_stack.push(bp2); + g_stack.push(bp1); + return ; + } + + cum_prob += UPM_ip2l_case2(i,l,j); + if (rnd < cum_prob) + { + energy += (EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l)); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n", "UPM_ip2l_case2",i,j,(EA_new()+2*EC_new()+EB_new()+ED3_new(j,i,i+1)+auPenalty_new(i+2,l))/100.0); + base_pair bp1(i+2,l,UP); + base_pair bp2(l+1,j-1,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return ; + } + } + int h1 = -1; + for (int h = i+3; h < j-1; ++h) + { + cum_prob += UPM_ijs2h(i,h,j); + if (rnd < cum_prob ) + { + energy += (ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new()); + h1 = h; + if (ss_verbose == 1) { + printf("%s(%d) %lf\n", "UPM_ijs2h",h1,(ED3_new(j,i,i+1)+ EA_new()+2*EC_new()+(h-i-1)*EB_new())/100.0); + } + break; + } + } + assert(h1!=-1); + + rnd = randdouble(); + cum_prob = 0; + for (int l = h1+1; l < j; ++l) + { + cum_prob += UPM_ijhl_case1(i,h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1)); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n","UPM_ijhl_case1",h1,l, (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l) + ED3_new(h1,l,l+1))/100.0); + base_pair bp1(h1,l,UP); + base_pair bp2(l+2,j-1,U1); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + + cum_prob += UPM_ijhl_case2(i,h1,l,j); + if (rnd < cum_prob) + { + energy += (ED5_new(h1,l,h1-1)+auPenalty_new(h1,l)); + if (ss_verbose == 1) + printf("%s(%d %d) %lf\n", "UPM_ijhl_case2",h1,l,(ED5_new(h1,l,h1-1)+auPenalty_new(h1,l))/100.0); + base_pair bp1(h1,l,UP); + base_pair bp2(l+1,j-1,U1D); + g_stack.push(bp1); + g_stack.push(bp2); + return; + } + } + assert(0); +} + +double rnd_structure(int* structure, int len) +{ + //printf("%lf %lf %lf\n", EA_new(), EB_new(), EC_new()); + srand(rand()); + base_pair first(1,len,U); + g_stack.push(first); + energy = 0.0; + + while (!g_stack.empty()) + { + base_pair bp = g_stack.top(); + // std::cout << bp; + g_stack.pop(); + + if (bp.type() == U) + rnd_u(bp.i,bp.j,structure); + else if (bp.type() == UD) + rnd_ud(bp.i,bp.j,structure); + else if (bp.type() == UP) + rnd_up(bp.i,bp.j,structure); + else if (bp.type() == U1) + rnd_u1(bp.i,bp.j,structure); + else if (bp.type() == U1D) + rnd_u1d(bp.i,bp.j,structure); + + } + return (double)energy/100.0; +} + +void batch_sample(int num_rnd, int length, double U) +{ + int* structure = new int[length+1]; + srand(time(NULL)); + std::map > uniq_structs; + + if (num_rnd > 0 ) { + printf("\nSampling structures...\n"); + int count; //nsamples =0; + for (count = 1; count <= num_rnd; ++count) + { + memset(structure, 0, (length+1)*sizeof(int)); + double energy = rnd_structure(structure, length); + + std::string ensemble(length+1,'.'); + for (int i = 1; i <= (int)length; ++ i) { + if (structure[i] > 0 && ensemble[i] == '.') + { + ensemble[i] = '('; + ensemble[structure[i]] = ')'; + } + } + //double myEnegry = -88.4; + //++nsamples; + //if (fabs(energy-myEnegry)>0.0001) continue; //TODO: debug + //++count; + + std::map >::iterator iter ; + if ((iter =uniq_structs.find(ensemble.substr(1))) != uniq_structs.end()) + { + std::pair& pp = iter->second; + pp.first++; + } + else { + uniq_structs.insert(make_pair(ensemble.substr(1),std::pair(1,energy))); + } + + // std::cout << ensemble.substr(1) << ' ' << energy << std::endl; + } + //std::cout << nsamples << std::endl; + int pcount = 0; + int maxCount = 0; std::string bestStruct; + double bestE = INFINITY; + + std::map >::iterator iter ; + for (iter = uniq_structs.begin(); iter != uniq_structs.end(); ++iter) + { + const std::string& ss = iter->first; + const std::pair& pp = iter->second; + const double& estimated_p = (double)pp.first/(double)num_rnd; + const double& energy = pp.second; + double actual_p = pow(2.718281,-1.0*energy/RT_)/U; + + printf("%s %lf %lf %lf %d\n",ss.c_str(),energy,actual_p,estimated_p,pp.first); + pcount += pp.first; + if (pp.first > maxCount) + { + maxCount = pp.first; + bestStruct = ss; + bestE = pp.second; + } + } + assert(num_rnd == pcount); + printf("\nMax frequency structure : \n%s e=%lf freq=%d p=%lf\n",bestStruct.c_str(),bestE,maxCount,(double)maxCount/(double)num_rnd); + + } + + delete [] structure; +} + +void set_single_stranded(int i, int j, int* structure) +{ + for(;i<=j;++i) + structure[i] = 0; +} + +void set_base_pair(int i, int j, int* structure) +{ + bool cond = j-i > TURN && canPair(RNA[i],RNA[j]); + assert(cond); + structure[i] = j; + structure[j] = i; +} diff --git a/gtfold-mfe/src/subopt_main.cc b/gtfold-mfe/src/subopt_main.cc new file mode 100644 index 0000000..96b2ac5 --- /dev/null +++ b/gtfold-mfe/src/subopt_main.cc @@ -0,0 +1,163 @@ +#include +#include +#include +#include +#include +#include +#include + +#include "loader.h" +#include "algorithms.h" +#include "subopt_traceback.h" +#include "global.h" +#include "utils.h" +#include "mfe_main.h" + + +using namespace std; + +static string seqfile = ""; +static string suboptFile = ""; +static double suboptDelta = 0; +static string outputPrefix = ""; +static string outputFile = ""; +static string outputDir = ""; +static string paramDir = ""; +static bool PARAM_DIR = false; +static void help(); + +void save_subopt_file(string outputFile, ss_map_t& ss_data, + const string& seq, int energy) +{ + ofstream outfile; + outfile.open(outputFile.c_str()); + char buff[4096]; + + sprintf(buff,"%s %6.2f", seq.c_str(), energy/100.0); + outfile << buff << std::endl; + for (ss_map_t::iterator it = ss_data.begin(); it!= ss_data.end(); ++it) + { + sprintf(buff,"%s %6.2f", (it->first).c_str(), it->second/100.0); + //outfile << it->first << '\t' << it->second/100.0 << std::endl; + outfile << buff << std::endl; + } + + outfile.close(); +} + +void parse_options(int argc, char** argv) { + int i; + + for(i=1; i 0) { + outputPrefix = outputPrefix.substr(pos+1); + } + + // and if an extension exists, remove it ... + if(outputPrefix.find(".") != string::npos) + outputPrefix.erase(outputPrefix.rfind(".")); + } + + // If output dir specified + if (!outputDir.empty()) { + outputFile += outputDir; + outputFile += "/"; + suboptFile += outputDir; + suboptFile += "/"; + } + // ... and append the .ct + outputFile += outputPrefix; + outputFile += ".ct"; + suboptFile += outputPrefix; + suboptFile += "_ss.txt"; + + +} + +static void help() { + printf("Usage: gtsubopt [OPTION]... FILE\n\n"); + + printf(" FILE is an RNA sequence file containing only the sequence or in FASTA format.\n\n"); + + printf("OPTIONS\n"); + printf(" --subopt NUM Calculate suboptimal structures within NUM kcal/mol\n"); + printf(" of the MFE. (Uses -d 2 treatment of dangling energies.)\n"); + printf("\n"); + printf(" -o, --output NAME Write output files with prefix given in NAME\n"); + printf(" -p --paramdir DIR Path to directory from which parameters are to be read\n"); + printf(" -h, --help Output help (this message) and exit.\n"); + printf(" -w, --workdir DIR Path of directory where output files will be written.\n"); + exit(-1); +} + +void subopt_main(int argc, char** argv) { + + string seq = ""; + parse_options(argc, argv); + + if (read_sequence_file(seqfile.c_str(), seq) == FAILURE) { + printf("Failed to open sequence file: %s.\n\n", seqfile.c_str()); + exit(-1); + } + init_fold(seq.c_str()); + + readThermodynamicParameters(paramDir.c_str(), PARAM_DIR, 0, 1, 0); + + int energy = calculate(seq.length()) ; + + double t1 = get_seconds(); + ss_map_t subopt_data = subopt_traceback(seq.length(), 100.0*suboptDelta); + t1 = get_seconds() - t1; + + printf("- thermodynamic parameters: %s\n", EN_DATADIR.c_str()); + printf("- input file: %s\n", seqfile.c_str()); + printf("- sequence length: %d\n", (int)seq.length()); + printf("\n"); + printf("Subopt traceback running time: %9.6f seconds\n", t1); + + printf("Subopt structures saved in %s\n", suboptFile.c_str()); + save_subopt_file(suboptFile, subopt_data, seq, energy); + + printf("+ calculating suboptimal structures within %f kcal/mol of MFE\n", suboptDelta); + printf("+ suboptimal structures file: %s\n", suboptFile.c_str()); + + free_fold(seq.length()); +} diff --git a/gtfold-mfe/src/subopt_traceback.cc b/gtfold-mfe/src/subopt_traceback.cc index 78bcc91..d67a852 100644 --- a/gtfold-mfe/src/subopt_traceback.cc +++ b/gtfold-mfe/src/subopt_traceback.cc @@ -1,406 +1,486 @@ /** - GTfold: compute minimum free energy of RNA secondary structure - Copyright (C) 2008 David A. Bader - http://www.cc.gatech.edu/~bader +GTfold: compute minimum free energy of RNA secondary structure +Copyright (C) 2008 David A. Bader +http://www.cc.gatech.edu/~bader - This program is free software: you can redistribute it and/or modify - it under the terms of the GNU General Public License as published by - the Free Software Foundation, either version 3 of the License, or - (at your option) any later version. +This program is free software: you can redistribute it and/or modify +it under the terms of the GNU General Public License as published by +the Free Software Foundation, either version 3 of the License, or +(at your option) any later version. - This program is distributed in the hope that it will be useful, - but WITHOUT ANY WARRANTY; without even the implied warranty of - MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - GNU General Public License for more details. +This program is distributed in the hope that it will be useful, +but WITHOUT ANY WARRANTY; without even the implied warranty of +MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +GNU General Public License for more details. - You should have received a copy of the GNU General Public License - along with this program. If not, see . - - @author prashant {pgaurav@gatech.edu} +You should have received a copy of the GNU General Public License +along with this program. If not, see . + +@author prashant {pgaurav@gatech.edu} */ #include -#include "subopt_traceback.h" #include "constants.h" -#include "data.h" -#include "algorithms.h" - -const char* lstr[] = {"W", "V", "VBI", "VM", "WM"}; - -void (*trace_func[5]) (int i, int j, ps_t& ps, ps_stack_t& gs, int energy); - -void print_stack(ps_stack_t temp) -{ - std::cout << "{\n"; - while (!temp.empty()) - { - ps_t ps = temp.top(); - temp.pop(); - ps.print(); - std::cout << '\n' ; - } - std::cout << "}\n"; +#include "energy.h" +#include "utils.h" +#include "global.h" +#include "subopt_traceback.h" + +#include +#include +#include + +//#define DEBUG 1 + +using std::pair; +using std::cout; +using std::endl; + +const char* lstr[] = {"W", "V", "VBI", "VM", "WM", "WMPrime", "fm", "fm1"}; + +void (*trace_func[8]) (int i, int j, ps_t& ps, ps_stack_t& gs); +static int delta = 0; +static int mfe = INFINITY_; +static int length = -1; +static int gflag = 0; + +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + +static int FM1[1500][1500] = {{0}}; +static int FM[1500][1500] = {{0}}; + +static inline int Ed5_new(int i, int j, int k) { + return (k!=0) ? Ed3(j, i, k) : Ed3(j,i,length); } -void process(ss_map_t& subopt_data, int energy, int len) -{ - int count = 0 ; - ps_stack_t gstack; - - // initialize the partial structure - // segment stack = {[1,n]}, label = W, list_bp = {} - ps_t first(0, len); - first.push(segment(5, len, lW, W[len])); - gstack.push(first); // initialize the partial structure stacka - - while (1) - { - if (gstack.empty()) break; // exit - - ps_t ps = gstack.top(); - gstack.pop(); - - if (ps.empty()) - { - //std::cout << ps.str << " dG =" << ps.ae_ << std::endl; - if (subopt_data.find(ps.str) == subopt_data.end()) - { - subopt_data.insert(std::make_pair(ps.str,ps.ae_)); - count++; - } - continue; - } - else - { - segment smt = ps.top(); - ps.pop(); - size_t s1 = gstack.size(); - - if (smt.j_ - smt.i_ >=4) - { - (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack, energy); - } - - if (gstack.size() == s1 && ps.total() <= energy) - { - ps_t ps1(ps); - gstack.push(ps1); - } - } - } +static inline int Ed3_new(int i, int j, int k) { + return (k!=length+1)?Ed5(j, i, k) : Ed5(j, i, 1); } -ss_map_t subopt_traceback(int len, int delta) -{ - trace_func[0] = traceW; - trace_func[1] = traceV; - trace_func[2] = traceVBI; - trace_func[3] = traceVM; - //trace_func[4] = traceWM; +void calculate_fm1() { + + //printf("length %d\n", length); + //printf("Ea: %d , Eb: %d , Ec: %d\n", Ea, Eb, Ec); + + for (int i = 1; i <= length; ++i) { + for (int j = i+1; j <= length; ++j) { + //printf("\nFinding FM1[%d][%d]\n", i, j); + int min = INFINITY_; + for (int l = i+TURN+1; l <= j; ++l) { + int d5 = Ed5_new(i,l,i-1); + int d3 = Ed3_new(i,l,l+1); + + int fm1 = V(i,l) + auPenalty(i,l) + d5 + d3 + Ec*(j-l) + Eb; + + //printf("l: %d\n", l); + //printf("V(%d, %d): %d, auPenalty: %d, Ed3(%d, %d, %d): %d, Ed5(%d, %d, %d): %d\n", + // i, l, V(i,l), + // auPenalty(i,l), + // i, l, i-1, d5, + // i, l, l+1, d3 + // ); + //printf("min: %d, fm1: %d, final_min: %d\n", min, fm1, MIN(min,fm1)); + min = MIN(min, fm1); + } + FM1[i][j] = min; + //printf("Value: %d ", FM1[i][j]); + } + //printf("\n"); + } - int mfe = W[len]; - int level = 0; +} - ss_map_t subopt_data; +void calculate_fm() { + + for (int i = 1; i <= length; ++i) { + for (int j = i+1; j <= length;++j) { + int min1 = INFINITY_; + for (int k = i+TURN+1; k <= j-TURN-1; ++k) { + int x = FM[i][k-1] + FM1[k][j]; + min1 = MIN(min1, x); + } + int min2 = INFINITY_; + for (int k = i; k <= j-TURN-1; ++k) { + int x = FM1[k][j] + Ec*(k-i); + min2 = MIN(min2, x); + } + FM[i][j] = MIN(min1, min2); + //printf("%d %d %d ", i, j, FM[i][j]); + } + //printf("\n"); + } +} - for (level = mfe; level <= mfe + delta; level += 10) - process(subopt_data, level, len); +#endif + +void process(ss_map_t& subopt_data, int len) { + int count = 0; + length = len; + +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + calculate_fm1(); + calculate_fm(); +#endif + + ps_stack_t gstack; + + + // initialize the partial structure, segment stack = {[1,n]}, label = W, list_bp = {} + ps_t first(0, len); + first.push(segment(1, len, lW, W[len])); + gstack.push(first); // initialize the partial structure stacka + + while (1) { + if (gstack.empty()) break; // exit + ps_t ps = gstack.top(); + gstack.pop(); + + if (ps.empty()) { + count++; + pair ins_result; + ins_result = subopt_data.insert(std::make_pair(ps.str,ps.ae_)); + if (ins_result.second == false) { + printf("Duplicate Structure!!!"); + exit(1); + } + //cout << ps.str << endl; + continue; + } + else { + segment smt = ps.top(); + ps.pop(); + + gflag = 0; + if (smt.j_ - smt.i_ > TURN) { + (*trace_func[smt.label_])(smt.i_, smt.j_, ps, gstack); + } + + // discarded current segment, using remaining ones + if (!gflag) { + ps_t ps1(ps); + gstack.push(ps1); + } + } + } + +#ifdef DEBUG + //printf("# SS = %d\n", count); +#endif +} - return subopt_data; +ss_map_t subopt_traceback(int len, int _delta) { + trace_func[0] = traceW; + trace_func[1] = traceV; + trace_func[2] = traceVBI; + trace_func[3] = traceVM; + trace_func[4] = traceWM; + trace_func[5] = traceWMPrime; +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + trace_func[6] = traceM; + trace_func[7] = traceM1; +#endif + + mfe = W[len]; + delta = _delta; + length = len; + + ss_map_t subopt_data; + process(subopt_data, len); + + return subopt_data; } -void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) -{ - // Hairpin Loop - if (eH(i,j) + ps.total() <= energy ) - { - // std::cout << "Hairpin " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.accumulate(eH(i,j)); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); - } - - // Stack - if (eS(i, j) + V(i+1, j-1) + ps.total() <= energy) - { - // std::cout << "Stack " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.push(segment(i+1, j-1, lV, V(i+1, j-1))); - ps1.accumulate(eS(i,j)); - ps1.update(i, j , '(', ')'); - push_to_gstack(gstack, ps1); - } - - // Internal Loop - if (VBI[i][j] + ps.total() <= energy ) - { - //std::cout << "Internal " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.push(segment(i, j, lVBI, VBI[i][j])); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); - } - - // Multiloop - if ( VM[i][j] + ps.total() <= energy ) - { - // std::cout << "Multi " << i << ' ' << j << std::endl; - ps_t ps1(ps); - ps1.push(segment(i, j, lVM, VM[i][j])); - ps1.update(i, j, '(', ')'); - push_to_gstack(gstack, ps1); - } +void traceV(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("V %d %d\n", i, j); + // Hairpin Loop + if (eH(i,j) + ps.total() <= mfe + delta) { + //printf("hairpin\n"); + ps_t ps1(ps); + ps1.accumulate(eH(i,j)); + ps1.update(i, j, '(', ')'); + push_to_gstack(gstack, ps1); + } + + // Stack + if (eS(i, j) + V(i+1, j-1) + ps.total() <= mfe + delta) { + //printf("stack %d %d %d %d\n", i, j, eS(i,j), V(i+1,j-1)); + ps_t ps1(ps); + ps1.push(segment(i+1, j-1, lV, V(i+1, j-1))); + ps1.accumulate(eS(i,j)); + ps1.update(i, j , '(', ')'); + push_to_gstack(gstack, ps1); + } + + // Internal Loop + if (VBI(i,j) + ps.total() <= mfe + delta) { + //printf("internal loop\n"); + traceVBI(i,j,ps,gstack); + } + +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION + int k; + + for (k = i+2; k <= j-TURN-1; ++k) { + + int kenergy1 = FM[i+1][k] + FM1[k+1][j-1]; + int d5 = Ed5(i, j, i+1); + int d3 = Ed3(i, j, j-1); + int aup = auPenalty(i,j); + int kenergy2 = d5 + d3 + aup + Ea + Eb; + int kenergy_total = kenergy1 + kenergy2; + if (i == 4 && j == 41) { + //printf("ps: "); + ps.print(); + //printf("\n"); + } + //printf("FM[%d][%d]: %d FM1[%d][%d]: %d\n", i+1, k, FM[i+1][k], k+1, j-1, FM1[k+1][j-1]); + //printf("Ed3(%d, %d, %d): %d Ed5(%d, %d, %d): %d Ea: %d\n", + // i,j,i+1, Ed5_new(i,j,i+1), i, j, j-1, Ed3_new(i,j,j-1), Ea); + //printf("Ed5(%d, %d, %d): %d Ed3(%d, %d, %d): %d Ea: %d %d %d\n", + // i,j,i+1, Ed5(i,j,i+1), i, j, i+1, Ed3(i,j,j-1), Ea, auPenalty(i,j), Eb); + //printf("kenergy_total: %d ps.total(): %d mfe+delta: %d i: %d j: %d k: %d\n", kenergy_total, + // ps.total(), mfe+delta, i, j, k); + if (kenergy_total + ps.total() <= mfe + delta) { + //printf("multiloop\n"); + ps_t ps1(ps); + ps1.push(segment(i+1,k, lM, FM[i+1][k])); + ps1.push(segment(k+1,j-1, lM1, FM1[k+1][j-1])); + ps1.accumulate(kenergy2); + ps1.update(i,j,'(',')'); + //printf("auPenalty: %d\n", auPenalty(i,j)); + push_to_gstack(gstack, ps1); + } + } +#else + + // Multiloop + if (VM(i,j) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.push(segment(i, j, lVM, VM(i,j))); + ps1.update(i, j, '(', ')'); + push_to_gstack(gstack, ps1); + } + +#endif } -void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) -{ - int p,q; - for (p = i+1; p < MIN(j-2-TURN, i+MAXLOOP+1); ++p) - { - int minq = j-i+p-MAXLOOP-2; - if (minq < p+1+TURN) minq = p+1+TURN; - - for (q = minq; q < j; q++) - { - if (V(p, q) + eL(i, j, p, q) + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(p, q, lV, V(p, q))); - ps1.accumulate(eL(i, j, p, q)); - push_to_gstack(gstack, ps1); - } - } - } +void traceVBI(int i, int j, ps_t& ps, ps_stack_t& gstack) { + int p,q; + + for (p = i+1; p <= MIN(j-2-TURN,i+MAXLOOP+1) ; p++) { + int minq = j-i+p-MAXLOOP-2; + if (minq < p+1+TURN) minq = p+1+TURN; + int maxq = (p==(i+1))?(j-2):(j-1); + for (q = minq; q <= maxq; q++) { + if (V(p, q) + eL(i, j, p, q) + ps.total() <= mfe + delta) { + ps_t ps1(ps); + ps1.push(segment(p, q, lV, V(p, q))); + ps1.update(i, j , '(', ')'); + ps1.accumulate(eL(i, j, p, q)); + push_to_gstack(gstack, ps1); + } + } + } } -void traceW(int h, int j, ps_t& ps, ps_stack_t& gstack, int energy) -{ - if ( (h>=j) || j == 0 || j == 1) return; - - for (int i = h; i < j; ++i) - { - int wim1 = MIN(0, W[i-1]); - - int wij = V(i,j) + auPenalty(i, j) + wim1; - if (wij + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(i, j, lV, V(i,j))); - if (wim1 <= 0 && i > 1) ps1.push(segment(1, i-1, lW, W[i-1])); - ps1.accumulate(auPenalty(i, j)); - push_to_gstack(gstack, ps1); - } - - int wijd = V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1; - if (wijd + ps.total() <= energy ) - { - ps_t ps3(ps); - ps3.push(segment(i, j-1, lV, V(i, j-1))); - if (wim1 <= 0 && i > 1) ps3.push(segment(1, i-1, lW, W[i-1])); - ps3.accumulate(auPenalty(i,j-1) + Ed5(j-1,i,j)); - push_to_gstack(gstack, ps3); - } - - int widj = V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1; - if (widj + ps.total() <= energy ) - { - ps_t ps4(ps); - ps4.push(segment(i+1, j, lV, V(i+1,j))); - if (wim1 <= 0 && i > 1) ps4.push(segment(1, i-1, lW, W[i-1])); - ps4.accumulate(auPenalty(i+1, j) + Ed3(j,i+1,i)); - push_to_gstack(gstack, ps4); - } - - int widjd = V(i+1, j-1) + auPenalty(i+1,j-1) + Ed3(j-1, i+1, i) + Ed5(j-1, i+1, j) + wim1; - if (widjd + ps.total() <= energy ) - { - ps_t ps2(ps); - ps2.push(segment(i+1, j-1, lV, V(i+1,j-1))); - if (wim1 <= 0 && i > 1) ps2.push(segment(1, i-1, lW, W[i-1])); - ps2.accumulate(auPenalty(i+1,j-1) + Ed3(j-1,i+1,i) + Ed5(j-1,i+1,j)); - push_to_gstack(gstack, ps2); - } - } - - if (W[j-1] + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(1, j-1, lW, W[j-1])); - push_to_gstack(gstack, ps1); - } +void traceW(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("W %d %d\n", i, j); + for (int l = i; l < j-TURN; ++l) { + int wim1 = MIN(0, W[l-1]); + int d3 = (l>i)?Ed3(j,l,l-1):0; + int d5 = (j(key, pss)); - continue; - } - - segment wm_seg = pss.top(); - pss.pop(); - - int i1 = wm_seg.i_; int j1 = wm_seg.j_; - - if (wm_seg.label_ == lV) - { - ps_t ps1(pss); - ps1.push_v(wm_seg); - wm_stack.push(ps1); - continue; - } - int h = i1; int k = j1; - - int wmij = V(h,k) + auPenalty(h,k) + Eb; - if (pss.total() + wmij <= energy ) - { - ps_t ps1(pss); - ps1.push_v(segment(h,k,lV, V(h,k))); - ps1.accumulate(auPenalty(h,k) + Eb); - wm_stack.push(ps1); - } - - int wmijd = V(h,k-1) + Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+ Ec ; - if (pss.total() + wmijd <= energy ) - { - ps_t ps1(pss); - ps1.push_v(segment(h,k-1,lV, V(h,k-1))); - ps1.accumulate(Ed5(k-1,h,k)+ auPenalty(h,k-1) +Eb+Ec); - wm_stack.push(ps1); - } - - int wmidj = V(h+1,k) + Ed3(k,h+1,h) + auPenalty(h+1, k) + Eb+Ec ; - if (pss.total() + wmidj <= energy ) - { - ps_t ps1(pss); - ps1.push_v(segment(h+1, k, lV, V(h+1,k))); - ps1.accumulate(Ed3(k,h+1,h) + auPenalty(h+1,k) +Eb+Ec); - wm_stack.push(ps1); - } - - int wmidjd = V(h+1, k-1) + Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec ; - if (pss.total() + wmidjd <= energy ) - { - ps_t ps1(pss); - ps1.push_v(segment(h+1, k-1, lV, V(h+1,k-1))); - ps1.accumulate(Ed3(k-1,h+1,h) + Ed5(k-1,h+1,k) + auPenalty(h+1,k-1) +Eb+ 2*Ec); - wm_stack.push(ps1); - } - - - if (pss.total() + WM[i1][j1-1] + Ec <= energy ) - { - ps_t ps1(pss); - ps1.push(segment(i1,j1-1, lWM, WM[i1][j1-1])); - ps1.accumulate(Ec); - wm_stack.push(ps1); - } - - if (pss.total() + WM[i1+1][j1] + Ec <= energy ) - { - ps_t ps1(pss); - ps1.push(segment(i1+1,j1, lWM, WM[i1+1][j1])); - ps1.accumulate(Ec); - wm_stack.push(ps1); - } - - for (int h = i1+1; h <= j1-1; ++h) - { - if (WM[i1][h] + WM[h+1][j1] + pss.total() <= energy ) - { - ps_t ps1(pss); - ps1.push(segment(i1, h, lWM, WM[i1][h])); - ps1.push(segment(h+1, j1, lWM, WM[h+1][j1])); - wm_stack.push(ps1); - } - } - } +#ifdef UNIQUE_MULTILOOP_DECOMPOSITION +void traceM1(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("M1 %d %d\n", i, j); + //if (i == 14) + //printf("%d %d\n", FM1[i][j-1], FM1[i][j-1] + Ec + ps.total()); + + if (FM1[i][j-1] + Ec + ps.total() <= mfe + delta) { + //printf("here1\n"); + ps_t ps1(ps); + ps1.push(segment(i, j-1, lM1, FM1[i][j-1])); + ps1.accumulate(Ec); + push_to_gstack(gstack, ps1); + } + + //printf("V(i,j):%d Ed5_new: %d Ed3_new: %d\n", V(i,j), Ed5_new(i,j,i-1), Ed3_new(i,j,j+1)); + int d5; + int d3; + int aup; + //d5 = (i != 1) ? Ed5(i,j,i-1) : Ed5(i,j,length); + //d3 = (j != length) ? Ed3(i,j,j+1) : Ed3(i,j,1); + d5 = Ed5_new(i, j, i-1); + d3 = Ed3_new(i, j, j+1); + aup = auPenalty(i,j); + + if (V(i,j) + d5 + d3 + aup + Eb + ps.total() <= mfe + delta) { + //printf("here2\n"); + ps_t ps1(ps); + ps1.push(segment(i, j, lV, V(i,j))); + ps1.accumulate(d5 + d3 + aup + Eb); + ps1.update(i,j,'(',')'); + //printf("auPenalty: %d\n", auPenalty(i,j)); + push_to_gstack(gstack, ps1); + } } -void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack, int energy) -{ - std::map filter; - int h; - - for (h = i+1; h <= j-1; ++h) - { - int dG; - int d5 = Ed5(i,j,i+1); - int d3 = Ed3(i,j,j-1); - int common = auPenalty(i,j) + Ea + Eb; - - dG = common + WM[i+1][h-1] + WM[h][j-1]; - if (dG + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1])); - ps1.push(segment(h, j-1, lWM, WM[h][j-1])); - ps1.accumulate(common) ; - traceWM(ps1, filter, energy); - } - - dG = common + WM[i+2][h-1] + WM[h][j-1] + d5 + Ec; - if (dG + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1])); - ps1.push(segment(h, j-1, lWM, WM[h][j-1])); - ps1.accumulate(common + d5 + Ec); - traceWM(ps1, filter, energy); - } - - dG = common + WM[i+1][h-1] + WM[h][j-2] + d3 + Ec; - if (dG + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(i+1,h-1, lWM, WM[i+1][h-1])); - ps1.push(segment(h, j-2, lWM, WM[h][j-2])); - ps1.accumulate(common + d3 + Ec); - traceWM(ps1, filter, energy); - } - - dG = common + WM[i+2][h-1] + WM[h][j-2] + d5 + d3 + 2*Ec; - if (dG + ps.total() <= energy ) - { - ps_t ps1(ps); - ps1.push(segment(i+2,h-1, lWM, WM[i+2][h-1])); - ps1.push(segment(h, j-2, lWM, WM[h][j-2])); - ps1.accumulate(common + d3 + d5 + 2*Ec) ; - traceWM(ps1, filter, energy); - } - } - - ps_map_t::iterator it ; - for (it = filter.begin(); it != filter.end(); ++it) - { - push_to_gstack(gstack, it->second); - } +void traceM(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("M %d %d\n", i, j); + int d5, d3; + int aup; + + if (FM[i][j-1] + Ec + ps.total() <= mfe + delta) { + //printf("here11\n"); + ps_t ps1(ps); + ps1.push(segment(i, j-1, lM, FM[i][j-1])); + ps1.accumulate(Ec); + push_to_gstack(gstack, ps1); + } + + //printf("V(i,j):%d Ed5_new: %d Ed3_new: %d\n", V(i,j), Ed5_new(i,j,i-1), Ed3_new(i,j,j+1)); + //d5 = (i != 1) ? Ed3(i,j,i-1) : Ed3(i,j,length); + //d3 = (j != length) ? Ed5(i,j,j+1) : Ed5(i,j,1); + d5 = Ed5_new(i, j, i-1); + d3 = Ed3_new(i, j, j+1); + aup = auPenalty(i,j); + if (V(i,j) + d5 + d3 + Eb + aup + ps.total() <= mfe + delta) { + //printf("here12\n"); + ps_t ps1(ps); + ps1.push(segment(i, j, lV, V(i,j))); + ps1.accumulate(d5 + d3 + Eb + aup); + ps1.update(i,j,'(',')'); + push_to_gstack(gstack, ps1); + } + + + for (int k = i+TURN+1; k <= j-TURN-1; ++k) { + + d5 = Ed5_new(k+1, j, k); + d3 = Ed3_new(k+1, j, j+1); + aup = auPenalty(k+1, j); + + if (FM[i][k] + V(k+1,j) + d5 + d3 + + Eb + aup + ps.total() <= mfe + delta) { + //printf("here3\n"); + ps_t ps1(ps); + ps1.push(segment(i, k, lM, FM[i][k])); + ps1.push(segment(k+1, j, lV, V(k+1,j))); + ps1.accumulate(d5 + d3 + Eb + aup); + //printf("auPenalty: %d\n", auPenalty(i,k)); + ps1.update(k+1,j,'(',')'); + push_to_gstack(gstack, ps1); + } + } + + for (int k = i; k <= j-TURN-1; ++k) { + + d5 = Ed5_new(k+1, j, k); + d3 = Ed3_new(k+1, j, j+1); + aup = auPenalty(k+1, j); + + if (V(k+1,j) + d5 + d3 + + Eb + Ec*(k-i+1) + aup + ps.total() <= mfe+delta) { + //printf("here4\n"); + ps_t ps1(ps); + ps1.push(segment(k+1, j, lV, V(k+1,j))); + ps1.accumulate(d5 + d3 + Eb + Ec*(k-i+1) + aup); + ps1.update(k+1, j, '(', ')'); + //printf("auPenalty: %d\n", auPenalty(k+1,j)); + push_to_gstack(gstack, ps1); + } + } +} + +#endif + +void traceWM(int i, int j, ps_t& ps, ps_stack_t& gstack) { + int d3 = (i==1)?Ed3(j,i,length):Ed3(j,i,i-1); + int d5 = Ed5(j,i,j+1); + + //printf("WM %d %d\n", i, j); + //printf("normal auPenalty: %d\n", auPenalty(i,j)); + if (V(i,j) + auPenalty(i, j) + Eb + d3 + d5 + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(auPenalty(i, j) + Eb + d3 + d5); + ps_new.push(segment(i,j, lV, V(i,j))); + push_to_gstack(gstack, ps_new); + } + + if (WMPrime[i][j] + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.push(segment(i,j, lWMPrime, WMPrime[i][j])); + push_to_gstack(gstack, ps_new); + } + + if (WM(i+1,j) + Ec + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(Ec); + ps_new.push(segment(i+1,j, lWM, WM(i+1,j))); + push_to_gstack(gstack, ps_new); + } + + if (WM(i,j-1) + Ec + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(Ec); + ps_new.push(segment(i,j-1, lWM, WM(i,j-1))); + push_to_gstack(gstack, ps_new); + } +} + +void traceWMPrime(int i, int j, ps_t& ps, ps_stack_t& gstack) { + for (int h = i+TURN+1 ; h <= j-TURN-2; h++) { + if (WM(i,h-1) + WM(h,j) + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.push(segment(i,h-1, lWM, WM(i,h-1))); + ps_new.push(segment(h,j, lWM, WM(h,j))); + push_to_gstack(gstack, ps_new); + } + } +} + +void traceVM(int i, int j, ps_t& ps, ps_stack_t& gstack) { + + //printf("VM %d %d\n", i, j); + int d3 = Ed3(i,j,j-1); + int d5 = Ed5(i,j,i+1); + + if (WMPrime[i+1][j-1] + Ea + Eb + auPenalty(i, j) + d3 + d5 + ps.total() <= mfe + delta) { + ps_t ps_new(ps); + ps_new.accumulate(Ea + Eb + auPenalty(i, j) + d3 + d5); + ps_new.push(segment(i+1,j-1, lWMPrime,WMPrime[i+1][j-1] )); + push_to_gstack(gstack, ps_new); + } } -void push_to_gstack(ps_stack_t& gstack , const ps_t& v) -{ - gstack.push(v); +void push_to_gstack(ps_stack_t& gstack, const ps_t& v) { + gflag = 1; + gstack.push(v); + //printf("Pushing to gstack: \n"); +// v.print(); + //printf("\n"); } diff --git a/gtfold-mfe/src/test_ss_constraint.c b/gtfold-mfe/src/test_ss_constraint.c new file mode 100644 index 0000000..e3bd2d3 --- /dev/null +++ b/gtfold-mfe/src/test_ss_constraint.c @@ -0,0 +1,155 @@ +/*This program is used for testing single stranded constraints. Functions written in this file can be used for other scripts as well +Author: Manoj Soni +Email: manoj6891@gmail.com +*/ +#include +#include +#include +//#include +#define LENGTH 10 +#define MAX_CONSTRS 10 + +void executeCommand(char* cmd){ + printf("Executing command: %s\n", cmd); + int returnVal = system(cmd); + printf("return value: %d\n", returnVal); + if(returnVal != 0){ + printf("Error: returnVal:%d, Exiting...\n", returnVal); + exit(-1); + } +} + +char* getToken(char* str, char* sep, int index){ + char * pch; + pch = strtok (str,sep); + char* fName = pch; + if(index==0) return fName; + if(index != -1){ + printf("Error: index can be only 0 or -1. 0 means first and -1 means last token\n"); + exit(-1); + } + while (pch != NULL) + { + //printf ("%s\n",pch); + fName=pch; + pch = strtok (NULL, sep); + } + printf("%s\n",fName); + return fName; +} + +char* getSeqName(char* seqFileName1){ + char* seqFileName = malloc(200); + strcpy(seqFileName,seqFileName1); + char* seq = getToken(seqFileName, "/", -1); + char* seqName = getToken(seq, ".", 0); + printf("seqName: %s\n",seqName); + return seqName; + +} + +void parseCtFileToFindForcedConstraintRegion(char* ctFileName, char* constrs[MAX_CONSTRS]){//printf("Entering parse method\n"); +//ct file contents are +//dG = -5.8 +//1 C 0 2 12 1 +//2 C 1 3 11 2 +//... ... ... +//then 1 is pairing with 12, 2 is pairing with 11 .. ? +//in other words, first column is i and 5th column is j for a pair (i,j) + //char* constrs[MAX_CONSTRS]; + int index=0; + FILE* ctFile = fopen(ctFileName, "r"); + char str[100]; + int arr[5]; + char c; + fscanf(ctFile, "%[^\n]", str);printf("first line: %s\n",str); + int start=-1, end=-1; + while(feof(ctFile)==0){ + fscanf(ctFile, "%d %c %d %d %d %d\n", &arr[0],&c,&arr[1],&arr[2],&arr[3],&arr[4]); + if(arr[3]!=0){ + if(start==-1){ start=arr[0]; end=arr[0];} + else end=arr[0]; + if (start!=-1 && end-start+1 >= LENGTH){ + //char* ss_constr; + char* ss_constr = (char*)malloc(30);//new char[30]; + sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1)); + constrs[index++] = ss_constr; + printf("constraint is: %s\n",ss_constr); + if(index>=MAX_CONSTRS) break; + start=-1; + } + } + else{ + if(start==-1) continue; + // char* ss_constr; + char* ss_constr = malloc(30);//new char[30]; + sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1)); + constrs[index++] = ss_constr; + printf("constraint is: %s\n",ss_constr); + if(index>=MAX_CONSTRS) break; + start=-1; + + } + // printf("line is: %d %c %d %d %d %d\n", arr[0],c,arr[1],arr[2],arr[3],arr[4]); + } + if(index>=MAX_CONSTRS) return ;//constrs; + //char* ss_constr; + char* ss_constr = malloc(30);//new char[30]; + if(start!=-1){ + sprintf(ss_constr, "%s%d%s%d", "P ", start, " 0 ", (end-start+1)); + printf("constraint is: %s\n",ss_constr); + constrs[index++] = ss_constr; + } + fclose(ctFile); + return ;//ss_constr; +} + +char* createConstraintFile(char* constrs[MAX_CONSTRS]){ + char* constrFileName = "constraints.txt"; + FILE* constrFile = fopen(constrFileName, "w+"); + int i; + for(i=0; i" if @ARGV < 1; + +my $seqName = $ARGV[0]; + +system("gcc -o test_ss_constraint test_ss_constraint.c"); +system("./test_ss_constraint $seqName"); diff --git a/gtfold-mfe/src/traceback.c b/gtfold-mfe/src/traceback.c index dff6ae9..6d461a8 100644 --- a/gtfold-mfe/src/traceback.c +++ b/gtfold-mfe/src/traceback.c @@ -17,341 +17,345 @@ along with this program. If not, see . */ -/* AUTHOR: Amrita Mathuriya August 2007-January 2009. - * This file tracebacks only one optimal secondary structure. Note that there may be more than one optimal secondary structures and the generated structure depends upon the choices taken during traceback. - * This file contains recursive functions. structure is a global integer array to store the optimal structure generated during traceback. - * Please note that - To understand the functions defined in this file, you first need to understand functions defined in algorithms.c file. As all those functions have a corresponding function here, for traceback the calculations done there. - * */ - -/* Modified by Sainath Mallidi August 2009 - "*/ -/* Modified traceback to handle constraints */ - -/* Modified by Prashant Gaurav , 09/07/2010 */ -/* Fixed the incorrect reporting of multiloop energy */ - #include #include #include +#include #include "data.h" #include "constants.h" -#include "algorithms.h" +#include "constraints.h" +#include "energy.h" +#include "global.h" #include "traceback.h" +#include "utils.h" +#include "shapereader.h" int total_en = 0; +int total_ex = 0; +int length = 0; -void trace(int len) { +void trace(int len) { int i; + for (i = 0; i <= len; i++) structure[i] = 0; - for (i = 0; i < LENGTH; i++) - structure[i] = 0; - + length = len; if (W[len] >= MAXENG) { - printf("\n No Structure "); + printf("- No Structure \n"); return; } + printf("\n"); + traceW(len); - printf("\n\n"); - - return; + if (g_verbose == 1) { + printf("- sum of energy of Loops: %12.2f kcal/mol\n", total_en/100.0); + printf("- sum of energy of External Loop: %12.2f kcal/mol\n", total_ex/100.0); + } + return; } void traceW(int j) { - int done, i, Wj,Wj_temp; - int wim1, flag, Widjd, Wijd, Widj, Wij; - - flag = 1; - done = 0; - Wj = INFINITY_; - int min_i=1; + int done = 0, i; + int wim1, flag = 1 ; + + if (j == 0 || j == 1) + return; - if (j == 0 || j == 1) return; - for (i = 1; i < j && !done; i++) { - wim1 = MIN ( 0, W[i-1] ); - flag = 1; - if (wim1 != W[i-1]) flag = 0; + if (j-i < TURN) continue; - Widjd = INFINITY_; - Wijd = INFINITY_; - Widj = INFINITY_; - - Wij = V[indx[i] + j] + auPen(RNA[i], RNA[j]) + wim1; - - if (constraints[i] <= 0 && constraints[j] <= 0) - Widjd = V[indx[i + 1] + j - 1] + auPen(RNA[i + 1], RNA[j - 1]) - + dangle[RNA[j - 1]][RNA[i + 1]][RNA[i]][1] - + dangle[RNA[j - 1]][RNA[i + 1]][RNA[j]][0] + wim1; - if (constraints[j] <= 0) - Wijd = V[indx[i] + j - 1] + auPen(RNA[i], RNA[j - 1]) - + dangle[RNA[j - 1]][RNA[i]][RNA[j]][0] + wim1; - if (constraints[i] <= 0) - Widj = V[indx[i + 1] + j] + auPen(RNA[i + 1], RNA[j]) - + dangle[RNA[j]][RNA[i + 1]][RNA[i]][1] + wim1; - Wj_temp=Wj; - - Wj = MIN(MIN(MIN(Wij, Widjd), MIN(Wijd, Widj)), Wj); - if (Wj_temp>Wj) min_i=i; - - if (W[j] == Wj) { - if (W[j] == Wij) { /* If the optimal secondary structure contain base pair (i,j) as paired.*/ - done = 1; - structure[i] = j; - structure[j] = i; - traceV(i, j); - if (flag || checkSS(1,i)) // Added this condition because if constraints are present, flag should be overridden - traceW(i - 1); - break; - } else if (W[j] == Widjd && constraints[i] <= 0 - && constraints[j] <= 0) { /* If base pair (i+1,j-1) is pairing and there is a dangling base on both its sides */ - done = 1; - structure[i + 1] = j - 1; - structure[j - 1] = i + 1; - traceV(i + 1, j - 1); - if (flag || checkSS(1,i)) traceW(i - 1); - break; - } else if (W[j] == Wijd && constraints[j] <= 0) { /* If base pair (i,j-1) pairs and base j is single stranded. */ - done = 1; - structure[i] = j - 1; - structure[j - 1] = i; - traceV(i, j - 1); - if (flag || checkSS(1,i) ) - traceW(i - 1); - break; - } else if (W[j] == Widj && constraints[i] <= 0) { /* If base pair (i+1,j) pairs and base i is single stranded. */ - done = 1; - structure[i + 1] = j; - structure[j] = i + 1; - traceV(i + 1, j); - if (flag || checkSS(1,i)) - traceW(i - 1); - break; + wim1 = MIN(0, W[i-1]); + flag = 1; + if ( wim1 != W[i-1] && canSSregion(0,i)) flag = 0; + + if (g_unamode||g_mismatch) { + if ((W[j] == V(i,j) + auPenalty(i, j) + wim1 && canStack(i,j)) || forcePair(i,j)) { + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i, j, auPenalty(i, j)/100.00); + total_ex += auPenalty(i, j); + traceV(i, j); + if (flag ) traceW(i - 1); + break; + } else if ((W[j] == V(i,j-1) + auPenalty(i,j-1) + Ed5(j-1,i,j) + wim1 && canSS(j) && canStack(i,j-1)) || forcePair(i, j-1)) { + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i, j-1, (auPenalty(i,j-1) + Ed5(j-1,i,j))/100.00); + total_ex += (auPenalty(i,j-1) + Ed5(j-1,i,j)); + traceV(i, j - 1); + if (flag ) traceW(i - 1); + break; + } else if ((W[j] == V(i+1,j) + auPenalty(i+1,j) + Ed3(j,i+1,i) + wim1 && canSS(i) && canStack(i+1,j)) || forcePair(i+1,j)){ + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j, (auPenalty(i+1,j) + Ed3(j,i+1,i))/100.00); + total_ex += (auPenalty(i+1,j) + Ed3(j,i+1,i)); + traceV(i + 1, j); + if (flag ) traceW(i - 1); + break; + } else if ((W[j] == V(i+1,j-1) + auPenalty(i+1, j-1) + Estacke(j-1,i+1) + wim1 && canSS(i) && canSS(j) && canStack(i+1,j-1)) || forcePair(i+1,j-1)) { + done = 1; + if (g_verbose == 1) printf("i %5d j %5d ExtLoop %12.2f\n", i+1, j-1, (auPenalty(i+1, j-1) + Estacke(j-1,i+1))/100.00); + total_ex += (auPenalty(i+1, j-1) + Estacke(j-1,i+1)); + traceV(i + 1, j - 1); + if (flag ) traceW(i - 1); + break; } + } else if (g_dangles == 2) { + int e_dangles = 0; + if (i>1) e_dangles += Ed3(j,i,i-1); + if (j= j) - return 0; - else { - for (h = i; h < j && !done; h++) { - a = WM[i][h] + WM[h + 1][j]; /* If WM(i,j) came from the summation of two WM terms */ - if (a == WM[i][j]) { - done = 1; - h1 = h; - break; - } + if (!done){ + if (g_unamode||g_mismatch) { + if (WM(i,j) == V(i,j) + auPenalty(i, j) + Eb && canStack(i,j)) { + eWM += traceV(i, j); + done = 1; + } else if (WM(i,j) == V(i+1, j) + Ed3(j,i + 1,i) + auPenalty(i+1, j) + Eb + Ec && canSS(i) && canStack(i+1,j)) { + eWM += traceV(i + 1, j); + done = 1; + } else if (WM(i,j) == V(i,j-1) + Ed5(j-1,i,j) + auPenalty(i,j-1) + Eb + Ec && canSS(j) && canStack(i,j-1)) { + done = 1; + eWM += traceV(i, j - 1); + } else if (WM(i,j) == V(i+1,j-1) + Estackm(j-1,i+1) + auPenalty(i+1, j-1) + Eb + 2*Ec && canSS(i) && canSS(j) && canStack(i+1,j-1)) { + done = 1; + eWM += traceV(i + 1, j - 1); + } + } else if (g_dangles == 2) { + int energy = V(i,j) + auPenalty(i, j) + Eb; + energy += (i==1)?Ed3(j,i,length):Ed3(j,i,i-1); + /*if (j +#include +#include +#include + +double get_seconds() { + struct timeval tv; + gettimeofday(&tv, NULL); + return (double) tv.tv_sec + (double) tv.tv_usec / 1000000.0; +} + +int is_valid_base(char c) { + return ( (c-'A' == 0) || (c-'a' == 0) || + (c-'C' == 0) || (c-'c' == 0) || + (c-'G' == 0) || (c-'g' == 0) || + (c-'U' == 0) || (c-'u' == 0)); +} + +char baseToDigit(const char* base) { + if (!strcmp(base, "A")) { + return '1'; + } + if (!strcmp(base, "C")) { + return '2'; + } + if (!strcmp(base, "G")) { + return '3'; + } + if (!strcmp(base, "U")) { + return '4'; + } + if (!strcmp(base, "N")) { + return '5'; + } + return (char) '0'; +} + +/** + * Encodes the given base to a number. + * + * Handles upper- and lower-case letters. + * + * @param base The character to encode + * @return The numerical encoding of the base + */ +unsigned char encode(char base) { + switch(base) { + case 'A': + case 'a': + return BASE_A; + case 'C': + case 'c': + return BASE_C; + case 'G': + case 'g': + return BASE_G; + case 'U': + case 'u': + case 'T': + case 't': + return BASE_U; + case 'N': + case 'n': + case 'R': + case 'r': + case 'Y': + case 'y': + case 'M': + case 'm': + case 'K': + case 'k': + case 'S': + case 's': + case 'W': + case 'w': + case 'B': + case 'b': + case 'D': + case 'd': + case 'H': + case 'h': + case 'V': + case 'v': + return BASE_A; + default: + return 'X'; + } +} + +/** + * Returns true if the given base is an A, C, G, U, or T + * @param base 'A', 'C', 'G', 'U', etc. + */ +int isWatsonCrickBase(char base) { + switch(base) { + case 'A': + case 'a': + case 'C': + case 'c': + case 'G': + case 'g': + case 'U': + case 'u': + case 'T': + case 't': + return true; + default: + return false; + } +} diff --git a/gtfold-mfe/tests/README b/gtfold-mfe/tests/README new file mode 100644 index 0000000..7e55fcb --- /dev/null +++ b/gtfold-mfe/tests/README @@ -0,0 +1,4 @@ +This directory contains the Test Framework for GTFold. +The complete documentation can be accessed here: +http://goo.gl/OliVA + diff --git a/gtfold-mfe/tests/config/root-logger.conf b/gtfold-mfe/tests/config/root-logger.conf new file mode 100644 index 0000000..7fa2cc7 --- /dev/null +++ b/gtfold-mfe/tests/config/root-logger.conf @@ -0,0 +1,7 @@ +#root-logger.conf +log4perl.rootLogger = INFO, myFILE +log4perl.appender.myFILE = Log::Log4perl::Appender::File +log4perl.appender.myFILE.filename = ../logs/error_log +log4perl.appender.myFILE.mode = append +log4perl.appender.myFILE.layout = Log::Log4perl::Layout::PatternLayout +log4perl.appender.myFILE.layout.ConversionPattern = [%p] (%F line %L) %m%n diff --git a/gtfold-mfe/tests/config/test-list.conf b/gtfold-mfe/tests/config/test-list.conf new file mode 100644 index 0000000..bff0017 --- /dev/null +++ b/gtfold-mfe/tests/config/test-list.conf @@ -0,0 +1,5 @@ +#Scoregtwithunafold +#ExitCodes +#CompareGTCTwithUNACT +#SuboptMatchStructures +ConstraintsVerification diff --git a/gtfold-mfe/tests/config/test-params.conf b/gtfold-mfe/tests/config/test-params.conf new file mode 100644 index 0000000..81ad292 --- /dev/null +++ b/gtfold-mfe/tests/config/test-params.conf @@ -0,0 +1,36 @@ +# Important directory variables +G_GTFOLD_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/src/ +G_UNAFOLD_DIR=/home/users/rbanga/rna/unafold/install/bin/ +G_RNAFOLD_DIR=/usr/local/bin/ +G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/16S_sequences/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/23S_sequences/ +#G_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/Other_sequences/ +G_WORK_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/work/ +G_TEST_LIST_FILE=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/config/test-list.conf + +# Sequence Inclusion Filters +#G_INCLUDE_SEQUENCES=rad +#G_INCLUDE_SEQUENCES=d.16.e.B.g* +#G_INCLUDE_SEQUENCES=d.16.e.B.m* +#G_INCLUDE_SEQUENCES=d.16.e.B.h* +#G_INCLUDE_SEQUENCES=d.16.e.E.bieneusi +#G_EXCLUDE_SEQUENCES=d.16.e.A.* +#G_EXCLUDE_SEQUENCES=d.16.e.B.ma* +#G_INCLUDE_SEQUENCES=acc1 +#G_INCLUDE_SEQUENCES=a.*j +#G_INCLUDE_SEQUENCES=a..tb* + +# Local Sequence Directories + +# Directory containing sequences for testing pseudoknot detection logic +L_EXITCODES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/exitcodes_sequences/ +L_SUBOPTMATCHSTRUCTURES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/5S_sequences/ +L_SUBOPTMATCHSTRUCTURES_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/subopt_sequences/ +L_SUBOPTMATCHSTRUCTURES_MIN_ENERGY=0 +L_SUBOPTMATCHSTRUCTURES_MAX_ENERGY=1 +L_SUBOPTMATCHSTRUCTURES_ENERGY_STRIDE=1 +L_SUBOPTMATCHSTRUCTURES_INCLUDE_SEQUENCES=d.5.a.H.* +L_CONSTRAINTSVERIFICATION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/constraints_sequences/ +L_CONSTRAINTSVERIFICATION_SEQUENCE_DIR=/home/users/rbanga/rna/git/gtfold/gtfold-mfe/tests/data/constraints_sequences/ diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq new file mode 100644 index 0000000..b8c95c6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.H.volcanii.seq @@ -0,0 +1,2 @@ +>d.16.a.H.volcanii +AUUCCGGUUGAUCCUGCCGGAGGUCAUUGCUAUUGGGGUCCGAUUUAGCCAUGCUAGUUGCACGAGUUCAUACUCGUGGCGAAAAGCUCAGUAACACGUGGCCAAACUACCCUACAGAGAACGAUAACCUCGGGAAACUGAGGCUAAUAGUUCAUACGGGAGUCAUGCUGGAAUGCCGACUCCCCGAAACGCUCAGGCGCUGUAGGAUGUGGCUGCGGCCGAUUAGGUAGACGGUGGGGUAACGGCCCACCGUGCCGAUAAUCGGUACGGGUUGUGAGAGCAAGAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACGGGGCGCAGCAGGCGCGAAACCUUUACACUGCACGCAAGUGCGAUAAGGGGACCCCAAGUGCGAGGGCAUAUAGUCCUCGCUUUUCUCGACCGUAAGGCGGUCGAGGAAUAAGAGCUGGGCAAGACCGGUGCCAGCCGCCGCGGUAAUACCGGCAGCUCAAGUGAUGACCGAUAUUAUUGGGCCUAAAGCGUCCGUAGCCGGCCACGAAGGUUCAUCGGGAAAUCCGCCAGCUCAACUGGCGGGCGUCCGGUGAAAACCACGUGGCUUGGGACCGGAAGGCUCGAGGGGUACGUCCGGGGUAGGAGUGAAAUCCCGUAAUCCUGGACGGACCACCGAUGGCGAAAGCACCUCGAGAAGACGGAUCCGACGGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGCUCGCUAGGUGUGACACAGGCUACGAGCCUGUGUUGUGCCGUAGGGAAGCCGAGAAGCGAGCCGCCUGGGAAGUACGUCCGCAAGGAUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGAGCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCUCACCAGCUCCGACUACAGUGAUGACGAUCAGGUUGAUGACCUUAUCACGACGCUGUAGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCACUUCUAAUUGCCAGCAGCAGUUUCGACUGGCUGGGUACAUUAGAAGGACUGCCGCUGCUAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAGUAUGCCCCGAAUGAGCUGGGCUACACGCGGGCUACAAUGGUCGAGACAAUGGGUUGCUAUCUCGAAAGAGAACGCUAAUCUCCUAAACUCGAUCGUAGUUCGGAUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCAUUUCAAUAGAGUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCAAAGCACCCGAGUGAGGUCCGGAUGAGGCCACCACACGGUGGUCGAAUCUGGGCUUCGCAAGGGGGCUUAAGUCGUAACAAGGUAGCCGUAGGGGAAUCUGCGGCUGGAUCACCUCCUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq new file mode 100644 index 0000000..e3a500d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.Halobacterium.sp.seq @@ -0,0 +1,2 @@ +>d.16.a.Halobacterium.sp +AUUCCGGUUGAUCCUGCCGGAGGCCAUUGCUAUCGGAGUCCGAUUUAGCCAUGCUAGUUGUGCGGGUUUAGACCCGCAGCGGAAAGCUCAGUAACACGUGGCCAAGCUACCCUGUGGACGGGAAUACUCUCGGGAAACUGAGGCUAAUCCCCGAUAACGCUUUGCUCCUGGAAGGGGCAAAGCCGGAAACGCUCCGGCGCCACAGGAUGCGGCUGCGGUCGAUUAGGUAGACGGUGGGGUAACGGCCCACCGUGCCCAUAAUCGGUACGGGUUGUGAGAGCAAGAGCCCGGAGACGGAAUCUGAGACAAGAUUCCGGGCCCUACGGGGCGCAGCAGGCGCGAAACCUUUACACUGUACGAAAGUGCGAUAAGGGGACUCCGAGUGUGAAGGCAUAGAGCCUUCACUUUUGUACACCGUAAGGUGGUGCACGAAUAAGGACUGGGCAAGACCGGUGCCAGCCGCCGCGGUAAUACCGGCAGUCCGAGUGAUGGCCGAUCUUAUUGGGCCUAAAGCGUCCGUAGCUGGCUGAACAAGUCCGUUGGGAAAUCUGUCCGCUUAACGGGCAGGCGUCCAGCGGAAACUGUUCAGCUUGGGACCGGAAGACCUGAGGGGUACGUCUGGGGUAGGAGUGAAAUCCUGUAAUCCUGGACGGACCGCCGGUGGCGAAAGCGCCUCAGGAGAACGGAUCCGACAGUGAGGGACGAAAGCUAGGGUCUCGAACCGGAUUAGAUACCCGGGUAGUCCUAGCUGUAAACGAUGUCCGCUAGGUGUGGCGCAGGCUACGAGCCUGCGCUGUGCCGUAGGGAAGCCGAGAAGCGGACCGCCUGGGAAGUACGUCUGCAAGGAUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAACCGGAGGAGCCUGCGGUUUAAUUGGACUCAACGCCGGACAUCUCACCAGCCCCGACAGUAGUAAUGACGGUCAGGUUGAUGACCUUACCCGAGGCUACUGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCUGUUAAGUCAGGCAACGAGCGAGACCCGCACUCCUAAUUGCCAGCAGUACCCUUUGGGUAGCUGGGUACAUUAGGUGGACUGCCGCUGCCAAAGCGGAGGAAGGAACGGGCAACGGUAGGUCAGUAUGCCCCGAAUGGGCUGGGCAACACGCGGGCUACAAUGGUCGAGACAAUGGGAAGCCACUCCGAGAGGAGGCGCUAAUCUCCUAAACUCGAUCGUAGUUCGGAUUGAGGGCUGAAACUCGCCCUCAUGAAGCUGGAUUCGGUAGUAAUCGCGUGUCAGCAGCGCGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCAAAUCACCCGAGUGGGGUUCGGAUGAGGCCGGCAUGCGCUGGUCAAAUCUGGGCUCCGCAAGGGGGAUUAAGUCGUAACAAGGUAGCCGUAGGGGAAUCUGCGGCUGGAUCACCUCCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq new file mode 100644 index 0000000..c32cdc8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.abyssi.seq @@ -0,0 +1,2 @@ +>d.16.a.P.abyssi +CGUACUCCCUUAAUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGUGCCGACCCCGAAAGGGGGAGGUAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCUAGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq new file mode 100644 index 0000000..14395d3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.P.horikoshii.seq @@ -0,0 +1,2 @@ +>d.16.a.P.horikoshii +AUUCCGGUUGAUCCUGCCGGAGGCCACUGCUAUGGGGGUCCGACUAAGCCAUGCGAGUCAAGGGGGCGUCCCUUCUGGGACGCCACCGGCGGACGGCUCAGUAACACGUCGGUAACCUACCCUCGGGAGGGGGAUAACCCCGGGAAACUGGGGCUAAUCCCCCAUAGGCCUGGGGUACUGGAAGGUCCCCAGGCCGAAAGGGAGCCGUAAGGCUCCGCCCGAGGAUGGGCCGGCGGCCGAUUAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGAAGAUCGGUACGGGCCGUGAGAGCGGGAGCCCGGAGAUGGACACUGAGACACGGGUCCAGGCCCUACGGGGCGCAGCAGGCGCGAAACCUCCGCAAUGCGGGAAACCGCGACGGGGGGACCCCCAGUGCCGUGCCUCUGGCACGGCUUUUCCGGAGUGUAAAAAGCUCCGGGAAUAAGGGCUGGGCAAGGCCGGUGGCAGCCGCCGCGGUAAUACCGGCGGCCCGAGUGGUGGCCACUAUUAUUGGGCCUAAAGCGGCCGUAGCCGGGCCCGUAAGUCCCUGGCGAAAUCCCACGGCUCAACCGUGGGGCUCGCUGGGGAUACUGCGGGCCUUGGGACCGGGAGAGGCCGGGGGUACCCCCGGGGUAGGGGUGAAAUCCUAUAAUCCCGGGGGGACCGCCAGUGGCGAAGGCGCCCGGCUGGAACGGGUCCGACGGUGAGGGCCGAAGGCCAGGGGAGCGAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAAGGAUGCGGGCUAGGUGUCGGGCGAGCUUCGAGCUCGCCCGGUGCCGUAGGGAAGCCGUUAAGCCCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUUAAAGGAAUUGGCGGGGGAGCACUACAAGGGGUGGAGCGUGCGGUUUAAUUGGAUUCAACGCCGGGAACCUCACCGGGGGCGACGGCAGGAUGAAGGCCAGGCUGAAGGUCUUGCCGGACGCGCCGAGAGGAGGUGCAUGGCCGCCGUCAGCUCGUACCGUGAGGCGUCCACUUAAGUGUGGUAACGAGCGAGACCCGCGCCCCCAGUUGCCAGUCCCUCCCGCUCGGGAGGGAGGCACUCUGGGGGGACUGCCGGCGAUAAGCCGGAGGAAGGGGCGGGCGACGGUAGGUCAGUAUGCCCCGAAACCCCCGGGCUACACGCGCGCUACAAUGGGCGGGACAAUGGGUGCCGACCCCGAAAGGGGGAGGUAAUCCCCUAAACCCGCCCUCAGUUCGGAUCGCGGGCUGCAACUCGCCCGCGUGAAGCUGGAAUCCCUAGUACCCGCGCGUCAUCAUCGCGCGGCGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCACUCCACCCGAGCGGGGCCUAGGUGAGGCCCGAUCUCCUUCGGGAGGUCGGGUCGAGCCUAGGCUCCGUGAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUACGGCUCGAUCACCUCCUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq new file mode 100644 index 0000000..0afb8fa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.a.S.solfataricus.2.seq @@ -0,0 +1,2 @@ +>d.16.a.S.solfataricus.2 +AAAUCCGGUUGAUCCUGCCGGACCCGACCGCUAUCGGGGUGGGGCUAAGCCAUGGGAGUCGUACGCUCCCGGGCAAGGGAGCGUGGCGGACGGCUGAGUAACACGUGGCUAACCUACCCUGAGGAGGGAGAUAACCCCGGGAAACUGGGGAUAAUCUCCCAUAGGCGAGGAGUCCUGGAACGGUUCCUCGCUGAAAGGCUCAUGGGCUAUUCCCCGCUCAUGAGCGCCUCAGGAUGGGGCUGCGGCCCAUCAGGUAGUUGGGGGGGUAAGGGCCCCCCAAGCCUAUAACGGGUAGGGGCCGUGAGAGCGGGAGCCCCCAGUUGGGCACUGAGACAAGGGCCCAGGCCCUACGGGGCGCACCAGGCGCGAAACGUCCCCAAUGCGCGGAAGCGUGAGGGCGCCACCCCGAGUGCUCCCGUAAGGGAGCUUUUCCCCGCUCUACAAAGGCGGGGGAAUAAGCGGGGGGCAAGUCUGGUGUCAGCCGCCGCGGUAAUACCAGCCCCGCGAGUGGUCGGGACUCUUACUGGGCCUAAAGCGCCCGUAGCCGGCCCGACAAGUCACUCCUUAAAGACCCCGGCUCAACCGGGGGAAUGGGGGUGAUACUGUCGGGCUAGGGGGCGGGAGAGGCCAGCGGUACUCCCGGAGUAGGGGCGAAAUCCUCAGAUCUCGGGAGGACCACCAGUGGCGAAAGCGGCUGGCUAGAACGCGCCCGACGGUGAGGGGCGAAAGCCGGGGCAGCAAAAGGGAUUAGAUACCCCUGUAGUCCCGGCUGUAAACAAUGCAGGCUAGGUGUCACAUGGGCUUAGAGCCCAUGUGGUGCCGCAGGGAAGCCGUUAAGCCUGCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUUAAAGGAAUUGGCGGGGGAGCACCACAAGGGGUGGAACCUGCGGCUCAAUUGGAGUCAACGCCUGGAAUCUUACUAGGGGAGACCGCAGGAUGACGGCCAGGCUAACGACCUUGCCUGACUCGCGGAGAGGAGGUGCAUGGCCGUCGCCAGCUCGUGUUGUGAAAUGUCCUGUUAAGUCAGGCAACGAGCGAGACCCCCACCACUAGUUGGUAUCCUGGUCUCCGGGCCGGGACCACACUAGUGGGACUGCCGGCGUAAGCCGGAGGAGGGAGGGGGCCACGGCAGGUCAGCAUGCCCCGAAACCCCUGGGCCGCACGCGGGUUACAAUGGCAGGGACAGCGGGAUUCCGACCCCGAAAGGGGAAGGUAAUCCCUUAAACCCUGCCGCAGUUGGGAUCGAGGGCUGAAACUCGCCCUCGUGAACGAGGAAUCCCUAGUAACCGCAGAUCAACAAUCUGCGGUGAAUACGUCCCUGCUCCUUGCACACACCGCCCGUCGCUCCACCCGAGUAGGAGAGGGGUGAGGCCCCUUGCCUUUGGGUGGGGGGUCGAGCUUCUCUCCUGCAAGGGGGGAGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq new file mode 100644 index 0000000..8d706e8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.globiformis.seq @@ -0,0 +1,2 @@ +>d.16.b.A.globiformis +UUUCAACGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAUCCGGUGCUUGCACCGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGAGUAACCUGCCCUUGACUCUGGGAUAAGCCUGGGAAACUGGGUCUAAUACCGGAUAUGACUCCUCAUCGCAUGGUGGGGGGUGGAAAGCUUUUUGUGGUUUUGGAUGGACUCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGUGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGUAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUUUGUCGCGUCUGCCGUGAAAGUCCGGGGCUCAACUCCGGAUCUGCGGUGGGUACGGGCAGACUAGAGUGAUGUAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGAUGGCGAAGGCAGGUCUCUGGGCAUUAACUGACGCUGAGGAGCGAAAGCAUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGUUGGGCACUAGGUGUGGGGGACAUUCCACGUUUUCCGCGCCGUAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGCGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCAAGGCUUGACAUGGACCGGACCGCCGCAGAAAUGUGGUUUCUCCUUUUGGGGCCGGUUCACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUCCAUGUUGCCAGCGCGUAAUGGCGGGGACUCAUGGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAAUCAUCAUGCCCCUUAUGUCUUGGGCUUCACGCAUGCUACAAUGGCCGGUACAAAGGGUUGCGAUACUGUGAGGUGGAGCUAAUCCCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCAAGUCACGAAAGUUGGUAACACCCGAAGCCGGUGGCCUAACCCCUUGUGGGAGGGAGCCGUCGAAGGUGGGACUGGCGAUUGGGACUAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq new file mode 100644 index 0000000..dca4e6e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.A.tumefaciens.seq @@ -0,0 +1,2 @@ +>d.16.b.A.tumefaciens +CUCAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAACGCCCCGCAAGGGGAGUGGCAGACGGGUGAGUAACGCGUGGGAAUCUACCGUGCCCUGCGGAAUAGCUCCGGGAAACUGGAAUUAAUACCGCAUACGCCCUACGGGGGAAAGAUUUAUCGGGGUAUGAUGAGCCCGCGUUGGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCCAUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGCAAGCCUGAUCCAGCCAUGCCGCGUGAGUGAUGAAGGCCUUAGGGUUGUAAAGCUCUUUCACCGGAGAAGAUAAUGACGGUAUCCGGAGAAGAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGCGCACGUAGGCGGAUAUUUAAGUCAGGGGUGAAAUCCCAGAGCUCAACUCUGGAACUGCCUUUGAUACUGGGUAUCUUGAGUAUGGAAGAGGUAAGUGGAAUUCCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGGAGGAACGCCAGUGGCGAAGGCGGCUUACUGGUCCAUUACUGACGCUGAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGUUAGCCGUCGGGCAGUAUACUGUUCGGUGGCGCAGCUAACGCAUUAAACAUUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGCAGAACCUUACCAGCUCUUGACAUUCGGGGUUUGGGCAGUGGAGACAUUGUCCUUCAGUUAGGCUGGCCCCAGAACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGCCCUUAGUUGCCAGCAUUUAGUUGGGCACUCUAAGGGGACUGCCGGUGAUAAGCCGAGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUACGGGCUGGGCUACACACGUGCUACAAUGGUGGUGACAGUGGGCAGCGAGACAGCGAUGUCGAGCUAAUCUCCAAAAGCCAUCUCAGUUCGGAUUGCACUCUGCAACUCGAGUGCAUGAAGUUGGAAUCGCUAGUAAUCGCAGAUCAGCAUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGUUUUACCCGAAGGUAGUGCGCUAACCGCAAGGAGGCAGCUAACCACGGUAGGGUCAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq new file mode 100644 index 0000000..040091c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Anabaena.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Anabaena.sp +GAAACGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGGUCUCUUCGGAGAUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUAGCUUCAGGUCGGGGACAACCACUGGAAACGGUGGCUAAUACCGGAUGUGCCGAAAGGUGAAAGAUUUAUUGCCUGAAGAUGAGCUCGCGUCUGAUUAGCUAGUUGGUGUGGUAAGAGCGCACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAGGGAGGAAGGCUCUUGGGUUGUAAACCUCUUUUCUCAGGGAAUAAAAAAAUGAAGGUACCUGAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCCGCAGGUGGCACUGUAAGUCUGCUGUUAAAGAGCAAGGCUCAACCUUGUAAAGGCAGUGGAAACUACAGAGCUAGAGUACGUUCGGGGCAGAGGGAAUUCCUGGUGUAGCGGUGAAAUGCGUAGAGAUCAGGAAGAACACCGGUGGCGAAAGCGCUCUGCUAGGCCGUAACUGACACUGAGGGACGAAAGCUAGGGGAGCGAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGCGUGGCUUGUAUCGACCCGAGCCGUGCCGGAGCCAACGCGUUAAGUAUCCCGCCUGGGGAGUACGCACGCAAGUGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAAGACUUGACAUGUCGCGAAUCUUCUUGAAAGGGAAGAGUGCCUUAGGGAGCGCGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUUUUAGUUGCCAGCAUUAAGUUGGGCACUCUAGAGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUACGUCUUGGGCUACACACGUACUACAAUGCUACGGACAGAGGGCAGCAAGCUAGCGAUAGCAAGCAAAUCCCGUAAACCGUAGCUCAGUUCAGAUCGCAGGCUGCAACUCGCCUGCGUGAAGGAGGAAUCGCUAGUAAUUGCAGGUCAGCAUACUGCAGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGCAACGCCCGAAGUCAUUACUCCAACUUUUAGGAGAGGAGGAUGCCUAAGGCAGUGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGUGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq new file mode 100644 index 0000000..b4e37d1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.bronchiseptica2.seq @@ -0,0 +1,2 @@ +>d.16.b.B.bronchiseptica2 +UGAACUGAAGAGUUUGAUCCUGGCUCAGAUUGAACGCUGGCGGGAUGCUUUACACAUGCAAGUCGGACGGCAGCACGGGCUUCGGCCUGGUGGCGAGUGGCGAACGGGUGAGUAAUGUAUCGGAACGUGCCCAGUAGCGGGGGAUAACUACGCGAAAGCGUGGCUAAUACCGCAUACGCCCUACGGGGGAAAGCGGGGGACCUUCGGGCCUCGCACUAUUGGAGCGGCCGAUAUCGGAUUAGCUAGUUGGUGGGGUAACGGCCUACCAAGGCGACGAUCCGUAGCUGGUUUGAGAGGACGACCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGGGGCAACCCUGAUCCAGCCAUCCCGCGUGUGCGAUGAAGGCCUUCGGGUUGUAAAGCACUUUUGGCAGGAAAGAAACGGCACGGGCUAAUAUCCUGUGCAACUGACGGUACCUGCAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGUGCGCAGGCGGUUCGGAAAGAAAGAUGUGAAAUCCCAGGGCUUAACCUUGGAACUGCAUUUUUAACUACCGGGCUAGAGUGUGUCAGAGGGAGGUGGAAUUCCGCGUGUAGCAGUGAAAUGCGUAGAUAUGCGGAGGAACACCGAUGGCGAAGGCAGCCUCCUGGGAUAACACUGACGCUCAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCCUAAACGAUGUCAACUAGCUGUUGGGGCCUUCGGGCCUUGGUAGCGCAGCUAACGCGUGAAGUUGACCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAUGAUGUGGAUUAAUUCGAUGCAACGCGAAAAACCUUACCUACCCUUGACAUGUCUGGAAUCCCGAAGAGAUUUGGGAGUGCUCGCAAGAGAACCGGAACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCAUUAGUUGCUACGAAAGGGCACUCUAAUGAGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUGGGUAGGGCUUCACACGUCAUACAAUGGUCGGGACAGAGGGUCGCCAACCCGCGAGGGGGAGCCAAUCCCAGAAACCCGAUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGUCGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUUUACCAGAAGUAGUUAGCCUAACCGCAAGGGGGGCGAUUACCACGGUAGGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq new file mode 100644 index 0000000..818a7c0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.burgdorferi.seq @@ -0,0 +1,2 @@ +>d.16.b.B.burgdorferi +AUAACGAAGAGUUUGAUCCUGGCUUAGAACUAACGCUGGCAGUGCGUCUUAAGCAUGCAAGUCAAACGGGAUGUAGCAAUACAUUCAGUGGCGAACGGGUGAGUAACGCGUGGAUGAUCUACCUAUGAGAUGGGGAUAACUAUUAGAAAUAGUAGCUAAUACCGAAUAAGGUCAGUUAAUUUGUUAAUUGAUGAAAGGAAGCCUUUAAAGCUCUCGCUUGUAGAUGAGUCUGCGUCUUAUUAGCUAGUUGGUAGGGUAAAUGCCUACCAAGGCAAUGAUAAGUAACCGGCCUGAGAGGGUGAACGGUCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGCUAAGAAUCUUCCGCAAUGGGCGGAAGCCUGACGGAGCGACACUGCGUGAAUGAAGAAGGUCGAAAGAUUGUAAAAUUCUUUUAUAAAUGAGGAAUAAGCUUUGUAGGAAAUGACAAAGUGAUGACGUUAAUUUAUGAAUAAGCCCCGGCUAAUUACGUGCCAGCAGCCGCGGUAAUACGUAAGGGGCGAGCGUUGUUCGGGAUUAUUGGGCGUAAAGGGUGAGUAGGCGGAUAUAUAAGUCUAUGCAUAAAAUACCACAGCUCAACUGUGGACCUAUGUUGGAAACUAUAUGUCUAGAGUCUGAUAGAGGAAGUUAGAAUUUCUGGUGUAAGGGUGGAAUCUGUUGAUAUCAGAAAGAAUACCGGAGGCGAAGGCGAACUUCUGGGUCAAGACUGACGCUGAGUCACGAAAGCGUAGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCUACGCUGUAAACGAUGCACACUUGGUGUUAACUAAAAGUUAGUACCGAAGCUAACGUGUUAAGUGUGCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCAGGGCUUGACAUAUAUAGGAUAUAGUUAGAGAUAAUUAUUCCCCGUUUGGGGUCUAUAUACAGGUGCUGCAUGGUUGUCGUCAGCUCGUGCUGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUAUCUGUUACCAGCAUGUAAUGGUGGGGACUCAGAUAAGACUGCCGGUGAUAAGUCGGAGGAAGGUGAGGAUGACGUCAAAUCAUCAUGGCCCUUAUGUCCUGGGCUACACACGUGCUACAAUGGCCUGUACAAAGCGAAGCGAAACAGUGAUGUGAAGCAAAACGCAUAAAGCAGGUCUCAGUCCGGAUUGAAGUCUGAAACUCGACUUCAUGAAGUUGGAAUCGCUAGUAAUCGUAUAUCAGAAUGAUACGGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACACCACCCGAGUUGAGGAUACCCGAAGCUAUUAUUCUAACCCGUAAGGGAGGAAGGUAUUUAAGGUAUGUUUAGUGAGGGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAAGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq new file mode 100644 index 0000000..4c06124 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.japonicum.seq @@ -0,0 +1,2 @@ +>d.16.b.B.japonicum +CCAACUUGAGAGUUUGAUCCUGGCUCAGAGCGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGGGCGUAGCAAUACGUCAGCGGCAGACGGGUGAGUAACGCGUGGGAACGUACCUUUUGGUUCGGAACAACACAGGGAAACUUGUGCUAAUACCGGAUAAGCCCUUACGGGGAAAGAUUUAUCGCCGAAAGAUCGGCCCGCGUCUGAUUAGCUAGUUGGUAGGGUAACGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACAUUGGGACUGAGACACGGCCCAAACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGCAACCCUGAUCCAGCCAUGCCGCGUGAGUGAUGAAGGCCCUAGGGUUGUAAAGCUCUUUUGUGCGGGAAGAUAAUGACGGUACCGCAAGAAUAAGCCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAUACGAAGGGGGCUAGCGUUGCUCGGAAUCACUGGGCGUAAAGGGUGCGUAGGCGGGUCUUUAAGUCAGGGGUGAAAUCCUGGAGCUCAACUCCAGAACUGCCUUUGAUACUGAAGAUCUUGAGUUCGGGAGAGGUGAGUGGAACUGCGAGUGUAGAGGUGAAAUUCGUAGAUAUUCGCAAGAACACCAGUGGCGAAGGCGGCUCACUGGCCCGAUACUGACGCUGAGGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAAUGCCAGCCGUUAGUGGGUUUACUCACUAGUGGCGCAGCUAACGCUUUAAGCAUUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGACGCAACGCGCAGAACCUUACCAGCCCUUGACAUGUCCAGGACCGGUCGCAGAGAUGUGACCUUCUCUUCGGAGCCUGGAACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGUCCUUAGUUGCUACCAUUUAGUUGAGCACUCUAAGGAGACUGCCGGUGAUAAGCCGCGAGGAAGGUGGGGAUGGCGUCAAGUCCUCAUGGCCCUUACGGGCUGGGCUACACACGUGCUACAAUGGCGGUGACAAUGGGAUGCUAAGGGGCGACCCUUCGCAAAUCUCAAAAAGCCGUCUCAGUUCGGAUUGGGCUCUGCAACUCGAGCCCAUGAAGUUGGAAUCGCUAGUAAUCGUGGAUCAGCACGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGGCUUUACCUGAAGACGGUGCGCUAACCAGCAAUGGAGGCAGCCGGCCACGGUAGGGUCAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq new file mode 100644 index 0000000..9433d8f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.B.subtilis.seq @@ -0,0 +1,2 @@ +>d.16.b.B.subtilis +UUUAUCGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGGACAGGUGGGAGCUUGCUCCCGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCUGUAAGACUGGGAUAACUCCGGGAAACCGGGGCUAAUACCGGAUGGUUGUUUGAACCGCAUGGUUCAAACAUAAAAGGUGGCUUCGGCUACCACUUACAGAUGGACCCGCGGCGCAUUAGCUAGUUGGUGAGGUAACGGCUCACCAAGGCAACGAUGCGUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGACGAAAGUCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUUUUCGGAUCGUAAAGCUCUGUUGUUAGGGAAGAACAAGUACCGUUCGAAUAGGGCGGUACCUUGACGGUACCUAACCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGGGCUCGCAGGCGGUUUCUUAAGUCUGAUGUGAAAGCCCCCGGCUCAACCGGGGAGGGUCAUUGGAAACUGGGGAACUUGAGUGCAGAAGAGGAGAGUGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAACACCAGUGGCGAAGGCGACUCUCUGGUCUGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGACUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGUCUUGACAUCCUCUGACAAUCCUAGAGAUAGGACGUCCCCUUCGGGGGCAGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGAUCUUAGUUGCCAGCAUUCAGUUGGGCACUCUAAGGUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGACCUGGGCUACACACGUGCUACAAUGGACAGAACAAAGGGCAGCGAAACCGCGAGGUUAAGCCAAUCCCACAAAUCUGUUCUCAGUUCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGCUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGUCGGUGAGGUAACCUUUUAGGAGCCAGCCGCCGAAGGUGGGACAGAUGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq new file mode 100644 index 0000000..f65748e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.pneumoniae.seq @@ -0,0 +1,2 @@ +>d.16.b.C.pneumoniae +UUUUCUGAGAAUUUGAUCUUAGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAAUAAUGACUUCGGUUGUUAUUUAGUGGCGGAAGGGUUAGUAGUACAUAGAUAAUCUGCCCUCAACUUGGGGAUAACGGUUGGAAACGAUCGCUAAUACCGAAUGUAGUGUAAUUAGGCAUCUAAUAUAUAUUAAAGAAGGGGAUCUUCGGACCUUUCGGUUGAGGAAGAGUUUAUGCGAUAUCAGCUUGUUGGUGGGGUAAAAGCCCACCAAGGCGAUGACGUCUAGGCGGAUUGAGAGAUUGACCGCCAACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGAAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCCUUAGGGUUGUAAAGCACUUUCGCCUGGGAAUAAGAGAGAUUGGCUAAUAUCCAAUCGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGAAAGUUAGAUGUUAAAUUUUGGGGCUCAACCCCAAGUCAGCAUUUAAAACUAUCUUUCUAGAGGAUAGAUGGGGAAAAGGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUAUACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUGGUCUCAACCCCAUCCGUGUCGGAGCUAACGUGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGGACCUUACCUGGACUUGACAUGUAUUUGACAACUGUAGAAAUACAGCUUUCCGCAAGGACAGAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAGCACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGUCCAGGGCGACACACGUGCUACAAUGGUUAGUACAGAAGGUAGCAAGAUCGUGAGAUGGAGCAAAUCCUAAAAGCUAGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCCAUAACGCCGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUACCUUAAGUCGUUGACUCAACCUAUUUAUAGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUGGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq new file mode 100644 index 0000000..4218316 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.psittaci.seq @@ -0,0 +1,2 @@ +>d.16.b.C.psittaci +UUUUCUGAGAAUUUGAUCUUGGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAAUAAUGACUUCGGUUGUUAUUUAGUGGCGGAAGGGUUAGUAAUACAUAGAUAAUCUGUCCUCAACUUGGGAAUAACGGUUGGAAACGACCGCUAAUACCGAAUGUGGUAUGUUUAGGCAUCUAAAACAUAUUAAAGAAGGGGAUCUUCGGACCUUUCGGUUGAGGGAGAGUCUAUGGGAUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCUUUGACGUCUAGGCGGAUUGAGAGAUUGACCGCCAACACUGGGACUGAGACACUGCCCAGACUUCUACGGAAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGAAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCUCUAGGGUUGUAAAGCACUUUCGCUUGGGAAUAAGAGAGAUUGGCUAAUAUCCAAUCGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGAAAGUUAGAUGUUAAAUCUUGGGGCUCAACCCCAAGCCAGCAUCUAAUACUAUCUUUCUAGAGGGUAGAUGGAGAAAAGGGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUACACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUAGUCUCAACCCUAUCCGUGUCGUAGCUAACGCGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGCUUGACAUGUAUUUGACCGCGGCAGAAAUGUCGUUUUCCGCAAGGACAGAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAACACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGCCCAGGGCUACACACGUGCUACAAUGGCCAGUACAGAAGGUAGCAAUAUCGUGAGAUGGAGCAAAUCCUCAAAGCUGGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCUAUAACGCCGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUGCCUUAAGUCGUUGACUCAACCUGCAAAGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUGGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq new file mode 100644 index 0000000..5084a44 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.testosteroni.seq @@ -0,0 +1,2 @@ +>d.16.b.C.testosteroni +CGAACUAUAGAGUUUGAUCCUGGCUCAGAUUGAACGCUGGCGGCAUGCUUUACACAUGCAAGUCGAACGGUAACAGGUCUUCGGAUGCUGACGAGUGGCGAACGGGUGAGUAAUACAUCGGAACGUGCCUAGUAGUGGGGGAUAACUACUCGAAAGAGUAGCUAAUACCGCAUGAGAUCUACGGAUGAAAGCAGGGGACCUUCGGGCCUUGUGCUACUAGAGCGGCUGAUGGCAGAUUAGGUAGUUGGUGGGGUAAAGGCUUACCAAGCCUGCGAUCUGUAGCUGGUCUGAGAGGACGACCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUGCCGCGUGCAGGAUGAAGGCCCUCGGGUUGUAAACUGCUUUUGUACGGAACGAAAAGCCUGGGGCUAAUAUCCCCGGGUCAUGACGGUACCGUAAGAAUAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGUGCGCAGGCGGUUUUGUAAGACAGUGGUGAAAUCCCCGGGCUCAACCUGGGAACUGCCAUUGUGACUGCAAGGCUAGAGUGCGGCAGAGGGGGAUGGAAUUCCGCGUGUAGCAGUGAAAUGCGUAGAUAUGCGGAGGAACACCGAUGGCGAAGGCAAUCCCCUGGGCCUGCACUGACGCUCAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCCUAAACGAUGUCAACUGGUUGUUGGGUCUUAACUGACUCAGUAACGAAGCUAACGCGUGAAGUUGACCGCCUGGGGAGUACGGCCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAUGAUGUGGUUUAAUUCGAUGCAACGCGAAAAACCUUACCCACCUUUGACAUGGCAGGAACUUACCAGAGAUGGUUUGGUGCUCGAAAGAGAACCUGCACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGCCAUUAGUUGCUACAUUCAGUUGAGCACUCUAAUGGGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCCUCAUGGCCCUUAUAGGUGGGGCUACACACGUCAUACAAUGGCUGGUACAAAGGGUUGCCAACCCGCGAGGGGGAGCUAAUCCCAUAAAGCCAGUCGUAGUCCGGAUCGCAGUCUGCAACUCGACUGCGUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGUCACGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGCGGGUCUCGCCAGAAGUAGGUAGCCUAACCGUAAGGAGGGCGCUUACCACGGCGGGGUUCGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq new file mode 100644 index 0000000..4ae3dc2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.C.trachomatis.L2.seq @@ -0,0 +1,2 @@ +>d.16.b.C.trachomatis.L2 +UUUUCUGAGAAUUUGAUCUUGGUUCAGAUUGAACGCUGGCGGCGUGGAUGAGGCAUGCAAGUCGAACGGAGCAAUUGUUUCGGCAAUUGUUUAGUGGCGGAAGGGUUAGUAAUGCAUAGAUAAUUUGUCCUUAACUUGGGAAUAACGGUUGGAAACGGCCGCUAAUACCGAAUGUGGCGAUAUUUGGGCAUCCGAGUAACGUUAAAGAAGGGGAUCUUAGGACCUUUCGGUUAAGGGAGAGUCUAUGUGAUAUCAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCUAUGACGUCUAGGCGGAUUGAGAGAUUGGCCGCCAACACUGGGACUGAGACACUGCCCAGACUCCUACGGGAGGCUGCAGUCGAGAAUCUUUCGCAAUGGACGGAAGUCUGACGAAGCGACGCCGCGUGUGUGAUGAAGGCUCUAGGGUUGUAAAGCACUUUCGCUUGGGAAUAAGAGAAGGCGGUUAAUACCCGCUGGAUUUGAGCGUACCAGGUAAAGAAGCACCGGCUAACUCCGUGCCAGCAGCUGCGGUAAUACGGAGGGUGCUAGCGUUAAUCGGAUUUAUUGGGCGUAAAGGGCGUGUAGGCGGAAAGGUAAGUUAGUUGUCAAAGAUCGGGGCUCAACCCCGAGUCGGCAUCUAAUACUAUUUUUCUAGAGGGUAGAUGGAGAAAAGGGAAUUUCACGUGUAGCGGUGAAAUGCGUAGAUAUGUGGAAGAACACCAGUGGCGAAGGCGCUUUUCUAAUUUAUACCUGACGCUAAGGCGCGAAAGCAAGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCUUGCCGUAAACGAUGCAUACUUGAUGUGGAUGGUCUCAACCCCAUCCGUGUCGGAGCUAACGCGUUAAGUAUGCCGCCUGAGGAGUACACUCGCAAGGGUGAAACUCAAAAGAAUUGACGGGGGCCCGCACAAGCAGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGGACCUUACCUGGGUUUGACAUGUAUAUGACCGCGGCAGAAAUGUCGUUUUCCGCAAGGACAUAUACACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUGCCAGCACUUAGGGUGGGAACUCUAACGAGACUGCCUGGGUUAACCAGGAGGAAGGCGAGGAUGACGUCAAGUCAGCAUGGCCCUUAUGCCCAGGGCGACACACGUGCUACAAUGGCCAGUACAGAAGGUAGCAAGAUCGUGAGAUGGAGCAAAUCCUCAAAGCUGGCCCCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGUCGGAAUUGCUAGUAAUGGCGUGUCAGCCAUAACGCCGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACAUCAUGGGAGUUGGUUUUACCUUAAGUCGUUGACUCAACCCGCAAGGGAGAGAGGCGCCCAAGGUGAGGCUGAUGACUAGGAUGAAGUCGUAACAAGGUAGCCCUACCGGAAGGUGGGGCUGGAUCACCUCCUUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq new file mode 100644 index 0000000..6f67dd9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.E.coli.seq @@ -0,0 +1,2 @@ +>d.16.b.E.coli +AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq new file mode 100644 index 0000000..7592528 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Frankia.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Frankia.sp +UUGAUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAGCGGGGAGCUUCGGCUCUCAGCGGCGAACGGGUGAGUAACACGUGGGCAACCUGCCCCGAGCUCUGGAAUAACCUCGGGAAACCGGGGCUAAUGCCGGAUAUGACAUUGCCGGGCAUCUGGUGGUGUGGAAAGAUUUAUCGGCUCGGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUGAUGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGCGGAAGCCUGACGCAGCGACGCCGCGUGGGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGACGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCACCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCCUGUUGCGUCGGCUGUGAAAACCCGGGGCUCAACUCCGGGCCUGCAGUCGAUACGGGCAGGCUAGAGUCCGGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGGUCUCUGGGCCGGAACUGACGCUAAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGUUGGGCGCUAGGUGUGGGGGACCUUCCACGGCCUCCGUGCCGCAGCUAACGCAUUAAGCGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCAGGGAAAUCUCGUAGAGAUACGGGGUCCGUAAGGGUCCUGCACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUCCUAUGUUGCCAGCGAGUCGUGUCGGGGACUCAUAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUACGUCCUGGGCUGCACACAUGCUACAAUGGCCGGUACAAAGGGCUGCGAUGCCGUGAGGUGGAGCGAAUCCCAAAAAGCCGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAAUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCUAACCCUUGUGGGGGGAGCCGUCGAAGGUGGGACCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq new file mode 100644 index 0000000..dada154 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.H.influenzae.seq @@ -0,0 +1,2 @@ +>d.16.b.H.influenzae +AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCUUAACACAUGCAAGUCGAACGGUAGCAGGAGAAAGCUUGCUUUCUUGCUGACGAGUGGCGGACGGGUGAGUAAUGCUUGGGAAUCUGGCUUAUGGAGGGGGAUAACGACGGGAAACUGUCGCUAAUACCGCGUAUUAUCGGAAGAUGAAAGUGCGGGACUGAGAGGCCGCAUGCCAUAGGAUGAGCCCAAGUGGGAUUAGGUAGUUGGUGGGGUAAAUGCCUACCAAGCCUGCGAUCUCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCGCAAUGGGGGGAACCCUGACGCAGCCAUGCCGCGUGAAUGAAGAAGGCCUUCGGGUUGUAAAGUUCUUUCGGUAUUGAGGAAGGUUGAUGUGUUAAUAGUACAUCAAAUUGACGUUAAAUACAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCGAGCGUUAAUCGGAAUAACUGGGCGUAAAGGGCACGCAGGCGGUUAUUUAAGUGAGGUGUGAAAGCCCUGGGCUUAACCUAGGAAUUGCAUUUCAGACUGGGUAACUAGAGUACUUUAGGGAGGGGUAGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAAUACCGAAGGCGAAGGCAGCCCCUUGGGAAUGUACUGACGCUCAUGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAAACGCUGUCGAUUUGGGGAUUGGGCUUAGAGCUUGGUGCCCGUAGCUAACGUGAUAAAUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUACUCUUGACAUCCUAAGAAGAGCUCAGAGAUGAGCUUGUGCCUUCGGGAACUUAGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGACUUGGUCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCGUAUACAGAGGGAAGCGAAGCUGCGAGGUGGAGCGAAUCUCAUAAAGUACGUCUAAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGAAUCAGAAUGUCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGUACCAGAAGUAGAUAGCUUAACCUUUUGGAGGGCGUUUACCACGGUAUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq new file mode 100644 index 0000000..042147f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.L.interrogans.seq @@ -0,0 +1,2 @@ +>d.16.b.L.interrogans +AACACGGAGAGUUUGAUCCUGGCUCAGAACUAACGCUGGCGGCGCGUCUUAAACAUGCAAGUCAAGCGGAGUAGCAAUACUCAGCGGCGAACGGGUGAGUAACACGUGGGUAAUCUUCCUCUGAGUCUGGGAUAACUUUCCGAAAGGGAAGCUAAUACUGGAUGGUCCCGAGAGAUCACAAGAUUUUUCGGGUAAAGAUUUAUUGCUCGGAGAUGAGCCCGCGUCCGAUUAGCUAGUUGGUGAGGUAAAGGCUCACCAAGGCGACGAUCGGUAGCCGGCCUGAGAGGGUGUUCGGCCACAAUGGAACUGAGACACGGUCCAUACUCCUACGGGAGGCAGCAGUUAAGAAUCUUGCUCAAUGGGGGGAACCUGAAGCAGCGACGCCGCGUGAACGAUGAAGGUCUUCGGAUUGUAAAGUUCAGUAAGCAGGGAAAAAUAAGCAGCAAUGUGAUGAUGGUACCUGCCUAAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAUGGUGCAAGCGUUGUUCGGAAUCAUUGGGCGUAAAGGGUGCGUAGGCGGACAUGUAAGUCAGGUGUGAAAACUGCGGGCUCAACUCGCAGCCUGCACUUGAAACUAUGUGUCUGGAGUUUGGGAGAGGCAAGUGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAGGAACACCAGUGGCGAAGGCGACUUGCUGGCCUAAAACUGACGCUGAGGCACGAAAGCGUGGGUAGUGAACGGGAUUAGAUACCCCGGUAAUCCACGCCCUAAACGUUGUCUACCAGUUGUUGGGGGUUUUAACCCUCAGUAACGAACCUAACGGAUUAAGUAGACCGCCUGGGGACUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGUCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAAAAACCUCACCUAGGCUUGACAUGGAGUGGAAUCAUGUAGAGAUACAUGAGCCUUCGGGCCGCUUCACAGGUGCUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCACCUUAUGUUGCCAUCAUUCAGUUGGGCACUCGUAAGGAACUGCCGGUGACAAACCGGAGGAAGGCGGGGAUGACGUCAAAUCCUCAUGGCCUUUAUGUCUAGGGCAACACACGUGCUACAAUGGCCGGUACAAAGGGUAGCCAACUCGCGAGGGGGAGCUAAUCUCAAAAAUCCGGUCCCAGUUCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCCCGGACCUUGUACACACCGCCCGUCACACCACCUGAGUGGGGAGCACCCGAAGUGGUCUUUGCCAACCGCAAGGAAGCAGACUACUAAGGUGAAACUCGUGAAGGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq new file mode 100644 index 0000000..1c5e7c6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.gallisepticum.seq @@ -0,0 +1,2 @@ +>d.16.b.M.gallisepticum +UUUUCUGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGCAUGCCUAAUACAUGCAAGUCGAUCGGAUGUAGCAAUACAUUAGAGGCGAACGGGUGAGUAACACGUAUCCAAUCUGCCUUAUAGUGGGGGAUAACUAGUCGAAAGAUUAGCUAAUACCGCAUAACAAGUUAACUAUCGCAUGAGAAUAACUUUAAAGAAGCAACUGCUUCGCUAUAAGAUGAGGGUGCGGCAUAUCAGCUAGUUGGUGAGGGUAAUGGCCCACCAAGGCGAUGACGUGUAGUUAUGCUGAGAGGUAGAAUAACCACAAUGGGACUGAGACACGGCCCAUACUCCUACGGGAGGCAGCAGUAGGGAAUUUUUCACAAUGGACGAAAGUCUGAUGGAGCAAUGCCGCGUGAACGAUGAAGGUCUUUUUAGAUUGUAAAGUUCUUUUAUUUGGGAAGAACAGUUAGUAGAGUGGAAAGCUAUUAAUUUGACUGUACCAUUUGAAUAAGUAACGACUAACUAUGUGCCAGCAGUCGCGGUAAUACAUAGGUUGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAACAAGCGCAGGCGGAUUAGAAAGUCUGGUGUUAAAAGCAAUUGCUUAACGAUUGUAUGCAUUGGAAACUUCUAGUCUAGAGUUUGGUAGAGAGUCCUGGAACUCCAUGUGGAGCGGUGAAAUGCGUAGAUAUAUGGAAGAACACCAGAGGCGAAGGCGAGGACUUGGGCCAAUACUGACGCUUAGGCUUGAAAGUGUGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCACACUGUAAACGAUGGAUGUUAAGUGUCGGAGCGAAUACUUCGGUGCUGCAGUUAACACAUUAAACAUCCUGCCUGAGUAGUACAUUCGCAAGAAUGAAACUCAAACGGAAUUGACGGGGACCCGCACAAGUGGUGGAGCAUGUUGCUUAAUUCGACGGUACACGAAAAACCUUACCUAGACUUGACAUCUUGGGCGAAGCUAUAGAAAUAUAGUGGAGGUCAACCCAAUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUACUUUGUCUAACGAGACUGCCAACGUAAGUUGGAGGAAGGUGGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGUCUAGGGCUGCAAACGUGCUACAAUGGCCAAUACAAACAGUUGCAAAUCCGUAAGGUGGAGCUAAUCUGUAAAGUUGGUCUCAGUUCGGAUUGAGGGCUGCAAUUCGCCCUCAUGAAGUCGGAAUCACUAGUAAUCGCGAAUCAGCCAUGUCGCGGUGAAUACGUUCUCGGGUCUUGUACACACCGCCCGUCAAACUAUGAGAGCUGGUAAUAUCUAAAACCGUGUUGCUAACCGCAAGGAAGCGCAUGUCUAGGGUAGGGCCGGUGAUUGGAGUUAAGUCGUAACAAGGUACCCCUACGAGAACGUGGGGGUGGAUUACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq new file mode 100644 index 0000000..b13dc11 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.genitalium.seq @@ -0,0 +1,2 @@ +>d.16.b.M.genitalium +CAAUUUUUUCUGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGCAUGCCUAAUACAUGCAAGUCGAUCGGAAGUAGCAAUACUUUAGAGGCGAACGGGUGAGUAACACGUAUCCAAUCUACCUUAUAAUGGGGGAUAACUAGUUGAAAAACUAGCUAAUACCGCAUAAGAACUUUAGUUCGCAUGAAUUAAAGUUGAAAGGACCUGCAAGGGUUCGUUAUUUGAUGAGGGUGCGCCAUAUCAGCUAGUUGGUAGGGUAAUGGCCUACCAAGGCAAUGACGUGUAGCUAUGCUGAGAAGUAGAAUAGCCACAAUGGGACUGAGACACGGCCCAUACUCCUACGGGAGGCAGCAGUAGGGAAUUUUUCACAAUGAGCGAAAGCUUGAUGGAGCAAUGCCGCGUGAACGAUGAAGGUCUUUUUGAUUGUAAAGUUCUUUUAUUUGGGAAGAAUGACUCUAGCAGGCAAUGGCUGGAGUUUGACUGUACCACUUUGAAUAAGUGACGACUAACUAUGUGCCAGCAGUCGCGGUAAUACAUAGGUCGCAAGCGUUAUCCGGAUUUAUUGGGCGUAAAGCAAGCGCAGGCGGAUUGAAAAGUCUGGUGUUAAAGGCAGCUGCUUAACAGUUGUAUGCAUUGGAAACUAUCAGUCUAGAGUGUGGUAGGGAGUUUUGGAAUUUCAUGUGGAGCGGUGAAAUGCGUAGAUAUAUGAAGGAACACCAGUGGCGAAGGCGAAAACUUAGGCCAUUACUGACGCUUAGGCUUGAAAGUGUGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCACACCGUAAACGAUAGAUACUAGCUGUCGGAGCGAUCCCUUCGGUAGUGAAGUUAACACAUUAAGUAUCUCGCCUGGGUAGUACAUUCGCAAGAAUGAAACUCAAACGGAAUUGACGGGGACCCGCACAAGUGGUGGAGCAUGUUGCUUAAUUCGACGGUACACGAAAAACCUUACCUAGACUUGACAUCCUUGGCAAAGUUAUGGAAACAUAAUGGAGGUUAACCGAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCGUUAGUUACAUUGUUUAACGAGACUGCUAAUGUAAAUUGGAGGAAGGAAGGGAUGACGUCAAAUCAUCAUGCCCCUUAUGUCUAGGGCUGCAAACGUGCUACAAUGGCCAAUACAAACAGUAGCCAACUUGUAAAAGUGAGCAAAUCUGAAAAGUUGGUCUCAGUUCGGAUUGAGGGCUGCAAUUCGUCCUCAUGAAGCUGGAAUCACUAGUAAUCGCGAAUCAGCUAUGUCGCGGUGAAUACGUUCUCGGGUCUUGUACACACCGCCCGUCAAACUAUGAAAGCUGGUAAUAUUUAAAAACGUGUUGCUAACCUUUAUUGGAAGCGCAUGUCAAGGAUAGCACCGGUGAUUGGAGUUAAGUCGUAACAAGGUACCCCUACGAGAACGUGGGGGUGGAUCACCUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq new file mode 100644 index 0000000..340893a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.hyopneumoniae.seq @@ -0,0 +1,2 @@ +>d.16.b.M.hyopneumoniae +CGCAAUCAUGAGAGUUUGAUCCUGGCUCAGGAUAAACGCUAGCUGUGUGCUUAAUACAUGCAUGUUGAACGGAAUAUUUUAGUUCGCUAAAAUAUUUAGUAGCAAAUGGGUGAGUAACACGUACCUAACCUACCUUUUGGACUGGGAUAACCAUUGGAAACAGUGGCUAAUACCAGAUAUGAUAAAAAUUUGCAUGAAUUUUUAUUCAAAGGAGCCUUCAAGCUUCACCAAGAAAUGGGGGUGCGCAACAUUAGUUAGUUGGUAGGGUAAAAGCCUACCAAGACGAUGAUGUUUAGCGGGGCCAAGAGGUUGUACCGCCACACUGGGAUUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUAAGGAAUAUUCCACAAUAAGCGAAAGCUUGAUGGAGCGACACAGCGUGCAGGAUGAAGUCUUUCGGGAUGUAAACUGCUGUUGUAAGGGAAGAAAAAACUAGAUAGGAAAUGCUCUAGUCUUGACGGUACCUUAUUAGAAAGCGACGGCAAACUAUGUGCCAGCAGCCGCGGUAAUACAUAGGUCGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGUCCGUAGGUUUUUUGUUAAGUUUAAAGUUAAAUGCUAAAGCUCAACUUUAGUCCGCUUUAGAUACUGGCAAAAUAGAAUUAUGAAGAGGUUAGCGGAAUUCCUAGUGGAGUGGUGGAAUACGUAGAUAUUAGGAAGAACACCAAUAGGCGAAGGCAGCUAACUGGUCAUAUAUUGACACUAAGGGACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAUCAUUAGUUGGUGGCAAAAGUCACUAACACAGCUAACGCGUUAAAUGAUCCGCCUGAGUAGUAUGCUCGCAAGAGUGAAACUUAAAGGAAUUGACGGGAACCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUUGAAGAUACGCGUAGAACCUUACCCACUCUUGACAUUCUCGCAAAACUAUAGAGAUAUAGCCGAGGCUAACGAGAUCACAGAUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUAGGUUAAGUCCUGCAACGAGCGCAACCCUUUUCUUUAGUUGCUAACAUUUAGUUGAGAACCCUAAAGAUACUGCCGGCGCAAGCCGGAGGAAGGUGGGGACGACGUCAAAUCAUCAUGCCUCUUACGAGUGGGGCAACACACGUGCUACAAUGGCUACUACAAAGAGCAGCAAAACAGUGAUGUCAAGCUAAUCUCAAAAAAGUAGUCUCAGUUCGGAUUGAAGUCUGCAACUCGACUUCAUGAAGUCGGAAUCGCUAGUAAUCGCAGGUCAGCUAUACUGCGGUGAAUACGUUCUCGGGUUUUGUACACACCGCCCGUCACACCAUGGGAGUUGGUAAUGCCCAAAGUCGGUGAGUUAACUUCGGAGACCAUUGCCUAAGGCAGGACCGAUGACUGGGGUGAAGUCGUAACAAGGUAUCCCUACGAGAACGUGGGGAUGGAACACCUCCUUUCUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq new file mode 100644 index 0000000..86728a4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.M.leprae.seq @@ -0,0 +1,2 @@ +>d.16.b.M.leprae +UUGUUUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGAAAGGUCUCUAAAAAAUCUUUUUUAGAGAUACUCGAGUGGCGAACGGGUGAGUAACACGUGGGUAAUCUGCCCUGCACUUCAGGGAUAAGCUUGGGAAACUGGGUCUAAUACCGGAUAGGACUUCAAGGCGCAUGUCUUGUGGUGGAAAGCUUUUUGCGGUGCAGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUGACGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGUGUCCGGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCGACGCCGCGUGGGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCACCAUCGACGAAGGUCUGGGUUUUCUCGGAUUGACGGUAGGUGGAGAAGAAGCACCGGCCAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGUGCGAGCGUUGUCCGGAAUUACUGGGCGUAAAGAGCUCGUAGGUGGUUUGUCGCGUUGUUCGUGAAAUCUCACGGCUUAACUGUGAGCGUGCGGGCGAUACGGGCAGACUAGAGUACUGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGGAAUGCGCAGAUAUCAGGAGGAACACCAGUGGCGAAGGCGGGUCUCUGGGCAGUAACUGACGCUGAGGAGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGUACUAGGUGUGGGUUUCCUUCCUUGGGAUCCGUGCCGUAGCUAACGCAUUAAGUACCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGUUUGACAUGCACAGGAUGCGUCUAGAGAUAGGCACUCCCUUGUGGCCUGUGUGCAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUCAUGUUGCCAGCACGUAAUGGUGGGGACUCGUGAGAGACUGCCGCGGUCAACUCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACACAUGCUACAAUGGCCGGUACAAAGGGCUGCGAUGCCGCAAGGUUAAGCGAAUCCUUUUAAAGCCGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGUCGGUAACACCCGAAGCCAGUGGCCUAACCCUCGGGAGGGAGCUGUCCAAGGUGGGAUCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq new file mode 100644 index 0000000..539e3c1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.pacificensis.seq @@ -0,0 +1,2 @@ +>d.16.b.P.pacificensis +AGAGUUUGAUCAUGGCUCAGAUUGAUCGCUGGCGGCAGGCUUAACACAUGCAAGUCGAGCGGAACGAUGAUAGCUUGCUAUCAGGCGUCGAGCGGCGGACGGGUGAGUAAUACUUAGGAAUCUACCUAGUAGUGGGGGAUAGCUCGGGGAAACUCGAAUUAAUACCGCAUACGUCCUACGGGAGAAAGCAGGGGAUCAUUAGACCUUGCGCUAUUAGAUGAGCCUAAGUCGGAUUAGCUAGAUGGUGGGGUAAAGGCCUACCAUGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACCGGGACUGAGACACGGCCCGGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGGGGAACCUGAUCCAGCCAUGCCGCGUGUGUGAAGAAGGCCUUUUGGUUGUAAAGCACUUUAAGCAGUGAAGAAGACUCUUCGGUUAAUACCCGGGGACGAUGACAUUAGCUGCAGAAUAAGCACCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGAGCGUAGGUGGCUUGAUAAGUCAGAUGUGAAAUCCCCGGGCUUAACCUGGGAACUGCAUCUGAAACUGUUAGGCUAGAGUAGGUGAGAGGGAAGUAGAAUUUCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUGAAGGAAUACCGAUGGCGAAGGCAGCUUCCUGGCAUCAUACUGACACUGAGGCUCGAAAGCGUGGGUAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCUACUAGUCGUUGGGUCCCUUGAGGACUUAGUGAUGCAGCUAACGCAAUAAGUAGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCCGGUCUUGACAUACACAGAAUCUUGUAGAGAUACGAGAGUGCCUUCGGGAAUUGUGAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCUUAGUUACCAGCGGGUUAAGCCGGGAACUCUAAGGAUACUGCCAGUGACAAACUGGAGGAAGGCGGGGACCACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGUAGGUACAGAGGGCAGCUACACAGCGAUGUGAUGCGAAUCUCAAAAAGCCUAUCGUAGUCCAGAUUGGAGUCUGCAACUCGACUCCAUGAAGUAGGAAUCGCUAGUAAUCGCGGAUCAGAAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUUGAUUGCACCAGAAGUGGUUAGCCUAACUUAGUGAGGGCGAUCACCACGGUGUGGUCGAUGACUGGGGUGAAGUCGUAACAAGGUAGCCCGUAGGGGAAACCUGCGGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq new file mode 100644 index 0000000..a0ca78a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.P.vulgaris.seq @@ -0,0 +1,2 @@ +>d.16.b.P.vulgaris +UAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAGCGGUAACAGGAGAAAGCUUGCUUUCUUGCUGACGAGCGGCGGACGGGUGAGUAAUGUAUGGGGAUCUGCCCGAUAGAGGGGGAUAACUACUGGAAACGGUGGCUAAUACCGCAUGACGUCUACGGACCAAAGCAGGGGCUCUUCGGACCUUGCGCUAUCGGAUGAACCCAUAUGGGAUUAGCUAGUAGGUGAGGUAAUGGCUCACCUAGGCAACGAUCUCUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUAGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGUGAUAAAGUUAAUACCUUUAUCAAUUGACGUUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUCAAUUAAGUCAGAUGUGAAAGCCCCGAGCUUAACUUGGGAAUUGCAUCUGAAACUGGUUGGCUAGAGUCUUGUAGAGGGGGGUAGAAUUCCACGUGUAGCGGUGAAAUGCGUAGAGAUGUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACAAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCUGUAAACGAUGUCGAUUUAGAGGUUGUGGUCUUGAACUGUGGCUUCUGGAGCUAACGCGUUAAAUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUACUCUUGACAUCCAGCGAAUCCUUUAGAGAUAGAGGAGUGCCUUCGGGAACGCUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGCGUAAUGGCGGGAACUCAAAGGAGACUGCCGGUGAUAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUACGAGUAGGGCUACACACGUGCUACAAUGGCAGAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGAACUCAUAAAGUCUGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUAGAUCAGAAUGCUACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq new file mode 100644 index 0000000..37dd472 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.erythropolis.seq @@ -0,0 +1,2 @@ +>d.16.b.R.erythropolis +UCAACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAGCGGUAAGGCCUUCGGGGUACACGAGCGGCGAACGGGUGAGUAACACGUGGGUGAUCUGCCCUGCACUUCGGGAUAAGCCUGGGAAACUGGGUCUAAUACCGGAUAUGACCUCCUAUCGCAUGGUGGGUGGUGGAAAGAUUUAUCGGUGCAGGAUGGGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGACGGGUAGCCGACCUGAGAGGGUGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGACGAAGCGCAAGUGACGGUACCUGCAGAAGAAGCACCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGAGCAAGCGUUGUCCGGAAUUACUGGGCGUAAAGAGUUCGUAGGCGGUUUGUCGCGUCGUUUGUGAAAACCAGCAGCUCAACUGCUGGCUUGCAGGCGAUACGGGCAGACUUGAGUACUGCAGGGGAGACUGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGGUCUCUGGGCAGUAACUGACGCUGAGGAACGAAAGCGUGGGUAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCGCUAGGUGUGGGUUCCUUCCACGGAAUCCGUGCCGUAGCUAACGCAUUAAGCGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGAUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGGUUUGACAUAUACCGGAAAGCUGCAGAGAUGUGGCCCCCCUUGUGGUCGGUAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUAUCUUAUGUUGCCAGCACGUUAUGGUGGGGACUCGUAAGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCCAGGGCUUCACACAUGCUACAAUGGCCAGUACAGAGGGCUGCGAGACCGUGAGGUGGAGCGAAUCCCUUAAAGCUGGUCUCAGUUCGGAUCGGGGUCUGCAACUCGACCCCGUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAACGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCAUGAAAGUCGGUAACACCCGAAGCCGGUGGCUUAACCCCUUGUGGGAGGGAGCCGUCGAAGGUGGGAUCGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq new file mode 100644 index 0000000..4cea7ad --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.felis.URRWXCal2.seq @@ -0,0 +1,2 @@ +>d.16.b.R.felis.URRWXCal2 +GACAGAAUCAAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUAUCGGUAUGCUUAACACAUGCAAGUCGGACGGACUAAUUGGGGCUUGCUCCAAUUAGUUAGUGGCAGACGGGUGAGUAACACGUGGGAAUCUGCCCAUCAGUACGGAAUAACUUUUAGAAAUAAAAGCUAAUACCGUAUAUUCUCUACAGAGGAAAGAUUUAUCGCUGAUGGAUGAGCCCGCGUCAGAUUAGGUAGUUGGUGAGGUAACGGCUCACCAAGCCGACGAUCUGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUACCGAGUGAGUGAUGAAGGCCCUAGGGUUGUAAAGCUCUUUUAGCAAGGAAGAUAAUGACGUUACUUGCAGAAAAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGAGUGCGUAGGCGGUUUAGUAAGUUGGAAGUGAAAGCCCGGGGCUUAACCUCGGAAUUGCUUUCAAAACUACUAAUCUAGAGUGUAGUAGGGGAUGAUGGAAUUCCUAGUGUAGAGGUGAAAUUCUUAGAUAUUAGGAGGAACACCGGUGGCGAAGGCGGUCAUCUGGGCUACAACUGACGCUGAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAGAUAUCGGAAGAUUCUCUUUCGGUUUCGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCUCGCACAAGCGGUGGAGCAUGCGGUUUAAUUCGAUGUUACGCGAAAAACCUUACCAACCCUUGACAUGGUGGUCGCGGAUCGCAGAGAUGCUUUCCUUCAGCUCGGCUGGACCACACACAGGUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCAUUCUUAUUUGCCAGCGGGUAAUGCCGGGAACUAUAAGAAAACUGCCGGUGAUAAGCCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGGGUUGGGCUACACGCGUGCUACAAUGGUGUUUACAGAGGGAAGCAAGACGGCGACGUGGAGCAAAUCCCUAAAAGACAUCUCAGUUCGGAUUGUUCUCUGCAACUCGAGAGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCUCGGGCCUUGUACACACUGCCCGUCACGCCAUGGGAGUUGGUUUUACCUGAAGGUGGUGAGCUAACGCAAGAGGCAGCCAACCACGGUAAAAUUAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUUACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq new file mode 100644 index 0000000..4768ec6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.R.prowazekii.seq @@ -0,0 +1,2 @@ +>d.16.b.R.prowazekii +AUCAAACUUGAGAGUUUGAUCCUGGCUCAGAACGAACGCUAUCGGUAUGCUUAACACAUGCAAGUCGAACGGAUUAACUAGAGCUCGCUUUAGUUAAUUAGUGGCAGACGGGUGAGUAACACGUGGGAAUCUACCCAUCAGUACGGAAUAACUUUUAGAAAUAAAAGCUAAUACCGUAUAUUCUCUACGGAGGAAAGAUUUAUCGCUGAUGGAUGGGCCCGCGUCAGAUUAGGUAGUUGGUGAGGUAAUGGCUCACCAAGCCGACGAUCUGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGGACAAUGGGCGAAAGCCUGAUCCAGCAAUACCGAGUGAGUGAUGAAGGCCUUAGGGUUGUAAAGCUCUUUUAGCAAGGAAGAUAAUGACGUUACUUGCAGAAAAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGAGGGGGCUAGCGUUGUUCGGAAUUACUGGGCGUAAAGAGUGCGUAGGCGGUUUAGUAAGUUGGAAGUGAAAGCCCGGGGCUUAACCUCGGAAUUGCUUUCAAAACUACUAAUCUAGAGUGUAGUAGGGGAUGAUGGAAUUCCUAGUGUAGAGGUGAAAUUCUUAGAUAUUAGGAGGAACACCGGUGGCGAAGGCGGUCAUCUGGGCUACAACUGACGCUGAUGCACGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAGAUAUCGGAGGAUUCUCUUUCGGUUUCGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGGUCGCAAGAUUAAAACUCAAAGGAAUUGACGGGGGCUCGCACAAGCGGUGGAGCAUGCGGUUUAAUUCGAUGUUACGCGAAAAACCUUACCAACCCUUGACAUGGUGGUUACGGAUUGCAGAGAUGCUUUCCUUCAGUUCGGCUGGGCCACACACAGGUGUUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUUCUUAUUUGCCAGUGGGUAAUGCCGGGAACUAUAAGAAAACUGCCGGUGAUAAGCCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGGCCCUUACGGGUUGGGCUACACGCGUGCUACAAUGGUGUUUACAGAGGGAAGCAAUACGGUGACGUGGAGCAAAUCCCUAAAAGACAUCUCAGUUCGGAUUGUUCUCUGCAACUCGAGAGCAUGAAGUUGGAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUACGUUCUCGGGCCUUGUACACACUGCCCGUCACGCCAUGGGAGUUGGUUUUACCUGAAGGUGGUGAGCUAACGCAAGAGGCAGCCAACCACGGUAAAAUUAGCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGCGGCUGGAUUACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq new file mode 100644 index 0000000..639b9c2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.acidiscabies.seq @@ -0,0 +1,2 @@ +>d.16.b.S.acidiscabies +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAUCACUCCUGCCUGCAUGGGCGGGGGUCGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGGAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCUGUGUUGCCAGCGUGCCCUUCGGGGUGACGGGGACUCACAGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAAGAGCUGCGAAACCGUGAGGUGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq new file mode 100644 index 0000000..1181b57 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.aureus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.aureus +UUUUAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCCUAAUACAUGCAAGUCGAGCGAACGGACGAGAAGCUUGCUUCUCUGAUGUUAGCGGCGGACGGGUGAGUAACACGUGGAUAACCUACCUAUAAGACUGGGAUAACUUCGGGAAACCGGAGCUAAUACCGGAUAAUAUUUUGAACCGCAUGGUUCAAAAGUGAAAGACGGUCUUGCUGUCACUUAUAGAUGGAUCCGCGCUGCAUUAGCUAGUUGGUAAGGUAACGGCUUACCAAGGCAACGAUGCAUAGCCGACCUGAGAGGGUGAUCGGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUAGGGAAUCUUCCGCAAUGGGCGAAAGCCUGACGGAGCAACGCCGCGUGAGUGAUGAAGGUCUUCGGAUCGUAAAACUCUGUUAUUAGGGAAGAACAUAUGUGUAAGUAACUGUGCACAUCUUGACGGUACCUAAUCAGAAAGCCACGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGUGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGCGCGUAGGCGGUUUUUUAAGUCUGAUGUGAAAGCCCACGGCUCAACCGUGGAGGGUCAUUGGAAACUGGAAAACUUGAGUGCAGAAGAGGAAAGUGGAAUUCCAUGUGUAGCGGUGAAAUGCGCAGAGAUAUGGAGGAACACCAGUGGCGAAGGCGACUUUCUGGUCUGUAACUGACGCUGAUGUGCGAAAGCGUGGGGAUCAAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGAGUGCUAAGUGUUAGGGGGUUUCCGCCCCUUAGUGCUGCAGCUAACGCAUUAAGCACUCCGCCUGGGGAGUACGACCGCAAGGUUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAAAUCUUGACAUCCUUUGACAACUCUAGAGAUAGAGCCUUCCCCUUCGGGGGACAAAGUGACAGGUGGUGCAUGGUUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAAGCUUAGUUGCCAUCAUUAAGUUGGGCACUCUAAGUUGACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACAUCAAAUCAUCAUGCCCCUUAUGAUUUGGGCUACACACGUGCUACAAUGGACAAUACAAAGGGCAGCGAAACCGCGAGGUCAAGCAAAUCCCAUAAAGUUGUUCUCAGUUCGGAUUGUAGUCUGCAACUCGACUACAUGAAGCUGGAAUCGCUAGUAAUCGUAGAUCAGCAUGCUACGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCACGAGAGUUUGUAACACCCGAAGCCGGUGGAGUAACCUUUUAGGAGCCAGCCGUCGAAGGUGGGACAAAUGAUUGGGGUGAAGUCGUAACAAGGUAGCCGUAUCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq new file mode 100644 index 0000000..2548398 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.bottropensis.seq @@ -0,0 +1,2 @@ +>d.16.b.S.bottropensis +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACAACACUCUCGGGCAUCCGAUGAGUGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUCGCCCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGGUGACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq new file mode 100644 index 0000000..bc38f32 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.diastatochromogenes.seq @@ -0,0 +1,2 @@ +>d.16.b.S.diastatochromogenes +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACAACCACUAGGGGCAUCUCUUGGUGGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAGUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq new file mode 100644 index 0000000..8d346c2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.eurythermus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.eurythermus +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCUCCUUCGGGAGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGAGCCUCCAAGGCAUCUUGGAGGUUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUUAGAGAUAGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq new file mode 100644 index 0000000..89dcb68 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.griseus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.griseus +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCUUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAACACUCUGUCCCGCAUGGGACGGGGUUAAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCUAGCUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGUUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUAUACCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGUAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUGCGCGAGGCGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq new file mode 100644 index 0000000..ea52e53 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.neyagawaensis.seq @@ -0,0 +1,2 @@ +>d.16.b.S.neyagawaensis +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGACGCGCUCGGGCAUCCGAUGUGCGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACGCCGGAAACACCCAGAGAUGGGUGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAGUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq new file mode 100644 index 0000000..a046f62 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.nodosus.seq @@ -0,0 +1,2 @@ +>d.16.b.S.nodosus +UUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCCUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGAGCCGGGGAGGCAUCUCCCUGGUUGGAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGCCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAGAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCGCGUCGCGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUUAGAGAUAGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCCAAGGUGGGACUGGCGAUUGGGACGAAAUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq new file mode 100644 index 0000000..f530e47 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.sampsonii.seq @@ -0,0 +1,2 @@ +>d.16.b.S.sampsonii +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCGCUUUCGGGCGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAUGACUGUCCAUCGCAUGGUGGAUGGUGUAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAGUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGUCUGGAGACAGGCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGUGAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq new file mode 100644 index 0000000..1155f53 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.scabiei.seq @@ -0,0 +1,2 @@ +>d.16.b.S.scabiei +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUUCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACGACACUCUCGGGCAUCCGAUGAGUGUGGAAAGCUCCGGCGGUGAAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAACGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCGAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACGGCCAGAGAUGGUCGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCAGGUACAAUGAGCUGCGAAGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCUGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCUAACCCGUAAGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq new file mode 100644 index 0000000..8cd1523 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.S.tendae.seq @@ -0,0 +1,2 @@ +>d.16.b.S.tendae +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAACCACUUCGGUGGGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUACUGACCCUCGCAGGCAUCUGCGAGGUUCGAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAAUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGCUUGUCACGUCGGUUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAGUCGAUACGGGCAGGCUAGAGUUCGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCGAUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGCACUAGGUGUGGGCAACAUUCCACGUUGUCCGUGCCGCAGCUAACGCAUUAAGUGCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAAGCAUCAGAGAUGGUGCCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCCCGUGUUGCCAGCAGGCCCUUGUGGUGCUGGGGACUCACGGGAGACCGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUACCGCAAGGUGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUCGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCCUUGUGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq new file mode 100644 index 0000000..d849fb4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Streptomyces.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Streptomyces.sp +CAUUCACGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGAUGAAGCCUUUCGGGGUGGAUUAGUGGCGAACGGGUGAGUAACACGUGGGCAAUCUGCCCUGCACUCUGGGACAAGCCCUGGAAACGGGGUCUAAUACCGGAUAAUACCUUCCCUCGCAUGGGGGUGGGUUCAAAGCUCCGGCGGUGCAGGAUGAGCCCGCGGCCUAUCAGCUUGUUGGUGAGGUAGUGGCUCACCAAGGCGACGACGGGUAGCCGGCCUGAGAGGGCGACCGGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGAAAGCCUGAUGCAGCGACGCCGCGUGAGGGAUGACGGCCUUCGGGUUGUAAACCUCUUUCAGCAGGGAAGAAGCGAAAGUGACGGUACCUGCAGAAGAAGCGCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGCGCAAGCGUUGUCCGGAAUUAUUGGGCGUAAAGAGCUCGUAGGCGGUCUGUCGCGUCGGAUGUGAAAGCCCGGGGCUUAACCCCGGGUCUGCAUUCGAUACGGGCAGACUAGAGUGUGGUAGGGGAGAUCGGAAUUCCUGGUGUAGCGGUGAAAUGCGCAGAUAUCAGGAGGAACACCGGUGGCGAAGGCGGAUCUCUGGGCCAUUACUGACGCUGAGGAGCGAAAGCGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGGUGGGAACUAGGUGUUGGCGACAUUCCACGUCGUCGGUGCCGCAGCUAACGCAUUAAGUUCCCCGCCUGGGGAGUACGGCCGCAAGGCUAAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCAGCGGAGCAUGUGGCUUAAUUCGACGCAACGCGAAGAACCUUACCAAGGCUUGACAUACACCGGAAACAUCCAGAGAUGGGUGCCCCCUUGUGGUCGGUGUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUCUGUGUUGCCAGCAUGCCCUUCGGGGUGAUGGGGACUCACAGGAGACUGCCGGGGUCAACUCGGAGGAAGGUGGGGACGACGUCAAGUCAUCAUGCCCCUUAUGUCUUGGGCUGCACACGUGCUACAAUGGCCGGUACAAUGAGCUGCGAUGCCGUGAGGCGGAGCGAAUCUCAAAAAGCCGGUCUCAGUUCGGAUUGGGGUCUGCAACUCGACCCCAUGAAGUCGGAGUUGCUAGUAAUCGCAGAUCAGCAUUGCUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGUCACGAAAGUCGGUAACACCCGAAGCCGGUGGCCCAACCCUUACGGGGAGGGAGCUGUCGAAGGUGGGACUGGCGAUUGGGACGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq new file mode 100644 index 0000000..0e4a9bb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.Synechococcus.sp.seq @@ -0,0 +1,2 @@ +>d.16.b.Synechococcus.sp +CAAAAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCGUGCUUAACACAUGCAAGUCGAACGGGCUCUUCGGAGCUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUGCCUACAGGACGGGGACAACAGUUGGAAACGACUGCUAAUACCCGAUGUGCCGAGAGGUGAAACAUUUAUGGCCUGUAGAUGAGCUCGCGUCUGAUUAGCUAGUUGGUGGGGUAAGGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGCAAGCGACGGAGCAACGCCGCGUGGGGGAGGAAGGUUUUUGGACUGUAAACCCCUUUUCUCAGGGAAGAAGAAAGUGACGGUACCUGAGGAAUAAGCCUCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGGAGAGGCAAGCGUUAUCCGGAAUUAUUGGGCGUAAAGCGCCUGCAGGCGGUUAAUCAAGUCUGUUGUCAAAGCGUGGGGCUCAACCUCAUACAGGCAAUGGAAACUGAUUGACUAGAGUAUGGUAGGGGUAGCGGGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAUAUCUGGAAGAACACCAGCGGCGAAAGCGCGCUACUGGGCCAUAACUGACGCUCAUGGACGAAAGCUAGGGGAGCGAAAGGGAUUAGAUACCCCUGUAGUCCUAGCCGUAAACGAUGAACACUAGGUGUUGCGUGAAUCGACCCGCGCAGUGCCGUAGCCAACGCGUUAAGUGUUCCGCCUGGGGAGUACGCACGCAAGUUGGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUCCCCCGAAUCUCUUGGAAACGAGAGAGUGCCUUCGGGAGCGGGGAGACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCACGUUUUUAGUUGCCAUCAUUCAGUUGGGCACUCUAGAGAAACUGCCGGUGACAAACCGGAGGAAGGUGUGGACGACGUCAAGUCAUCAUGCCCCUUACAUCCUGGGCUACACACGUACUACAAUGCUCCGGACAGCGAGACGCGAAGCCGCGAGGUGAAGCAAAUCUCCCAAACCGGGGCUCAGUUCAGAUUGCAGGCUGCAACUCGCCUGCAUGAAGGCGGAAUCGCUAGUAAUCGCAGGUCAGCAUACUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGUUGGCCAUGCCCGAAGUCGUUACCCUAACCGUUCGCGGAGGGGGGCGCCGAAGGUAGGGCUGAUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGUGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq new file mode 100644 index 0000000..2d0e8e9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.maritima.seq @@ -0,0 +1,2 @@ +>d.16.b.T.maritima +UAUAUGGAGGGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAACACAUGCAAGUCGAGCGGGGGAAACUCCCUUCGGGGAGGAGUACCCAGCGGCGGACGGGUGAGUAACACGUGGGUAACCUGCCCUCCGGAGGGGGAUAACCAGGGGAAACCCUGGCUAAUACCCCAUACGCUCCAUCAACGCAAGUUGGUGGAGGAAAGGGGCGUUUGCCCCGCCGGAGGAGGGGCCCGCGGCCCAUCAGGUAGUUGGUGGGGUAACGGCCCACCAAGCCGACGACGGGUAGCCGGCCUGAGAGGGUGGUCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUGGGGAAUCUUGGACAAUGGGGGAAACCCUGAUCCAGCGACGCCGCGUGCGGGACGAAGCCCUUCGGGGUGUAAACCGCUGUGGCGGGGGAAGAAUAAGGUAGGGAGGAAAUGCCCUACCGAUGACGGUACCCCGCUAGAAAGCCCCGGCUAACUACGUGCCAGCAGCCGCGGUAAUACGUAGGGGGCAAGCGUUACCCGGAUUUACUGGGCGUAAAGGGGGCGUAGGCGGCCUGGUGUGUCGGAUGUGAAAUCCCACGGCUCAACCGUGGGGCUGCAUCCGAAACUACCAGGCUUGGGGGCGGUAGAGGGAGACGGAACUGCCGGUGUAGGGGUGAAAUCCGUAGAUAUCGGCAGGAACGCCGGUGGGGAAGCCGGUCUCCUGGGCCGACCCCGACGCUGAGGCCCGAAAGCCAGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCUGGCUGUAAACGAUGCCCACUAGGUGUGGGGGGGUAAUCCCUCCGUGCUGAAGCUAACGCGUUAAGUGGGCCGCCUGGGGAGUACGCCCGCAAGGGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCGUGUGGUUUAAUUGGAUGCUAAGCCAAGAACCUUACCAGGGCUUGACAUGCCGGUGGUACCUCCCCGAAAGGGGUAGGGACCCAGUCCUUCGGGACUGGGAGCCGGCACAGGUGGUGCACGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUGCCCCUAGUUGCCAGCGGUUCGGCCGGGCACUCUAGGGGGACUGCCGGCGACGAGCCGGAGGAAGGAGGGGAUGACGUCAGGUACUCGUGCCCCUUAUGCCCUGGGCGACACACGCGCUACAAUGGGCGGUACAAUGGGUUGCGACCCCGCGAGGGGGAGCCAAUCCCCAAAGCCGCCCUCAGUUCGGAUCGCAGGCUGCAACCCGCCUGCGUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCACCCGAGUCGGGGGCUCCCGAAGACACCUACCCCAACCCGAAAGGGAGGGGGGGUGUCGAGGGAGAACCUGGCGAGGGGGGCGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq new file mode 100644 index 0000000..23d8958 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.b.T.pallidum.A.seq @@ -0,0 +1,2 @@ +>d.16.b.T.pallidum.A +AUGAUGGAGAGUUUGAUCCUGGCUCAGAACGAACGCUGGCGGUGCGUUUUAAGCAUGCAAGUCGAACGGCAAGGAAGCGAAUUUUCGUUUCUCUAGAGUGGCGGACUGGUGAGUAACGCGUGGGUAAUCUGCCUUUGAGAUGGGGAUAGCCUCUAGAAAUAGGGGGUAAUACCGAAUACGCUCUUUUGGACGUAGUCUUUGAGAGGAAAGGGGCUGCGGCCUCGCUCAGAGAUGAGCCUGCGACCCAUUAGCUUGUUGGUGGGGUAAUGGCCUACCAAGGCGUCGAUGGGUAUCCGACCUGAGAGGGUGACCGGACACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGCUAAGAAUAUUCCGCAAUGGGCGAAAGCCUGACGGAGCGACACCGCGUGGAUGAGGAAGGUCGAAAGAUUGUAAAGUUCUUUUGCCGACGAAGAAUGAGGACGGGAGGGAAUGCCCGUUUGAUGACGGUAGUCGUGCGAAUAAGCCCCGGCUAAUUACGUGCCAGCAGCCGCGGUAACACGUAAGGGGCGAGCGUUGUUCGGAAUUAUUGGGCGUAAAGGGCAUGCAGGCGGACUGGUAAGCCUGGUGUGAAAUCCCCGAGCUCAACUUGGGAACUGCACUGGGUACUGCUGGUCUAGAAUCACGGAGGGGAAACCGGAAUUCCAAGUGUAGGGGUGGAAUCUGUAGAUAUUUGGAAGAACACCGGUGGCGAAGGCGGGUUUCUGGCCGAUGAUUGACGCUGAGGUGCGAAGGUGUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCACACAGUAAACGAUGUACACUAGGUGUUGGGGCAUGAGUCUCGGCGCCGACGCGAACGCAUUAAGUGUACCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGAUACGCGAGGAACCUUACCCGGGUUUGACAUCAAGAGGAGCGCCGUAGAAAUGCGGUGGCGUAGCGAUACGCCUCUUGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCUACUGCCAGUUGCCAGCAAGUGGUGUUGGGGACUCUGGCGGAACUGCCGGUGACAAACCGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUGGCCCUUAUGUCCGGGGCUACACACGUGCUACAAUGGUUGCUACAGAGCGAUGCGAGGUUGUGAAGUGGAGCAAACCGCAAAAAGGCAAUCGUAGUCCGGAUUGAAGUCUGAAACUCGACUUCAUGAAGUUGGAAUCGCUAGUAAUCGCACAUCAGCAUGGUGCGGUGAAUGUGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUCCGAGUUGGAGAUACCCGAAGUCACUAGCCUAACCCGCAAGGGAGGGCGGUGCCGAAGGUAUGUUUGGUAAGGAGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq new file mode 100644 index 0000000..575befd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.caldarium.seq @@ -0,0 +1,2 @@ +>d.16.c.C.caldarium +UAUAAUGGAGAGUUUGAUCCUGGCUCAGGAUUAACGCUGGCGGUAUGCCUAACACAUGCAAGUCGUACGAGAAUUUUAUUCUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCUCUAGGAGGGGGAUAACAGUUGGAAACGAUUGCUAAAACCCCAUAUGCCAUUAUUGGUGAAAAAGAUUUAUCUGCCUGGAGAUGAGCUCGCGGCUGAUUAGCUAGUUGGUAGGGUAAUGGCUUACCAAGGCAACGAUCAGUAGCUGGUCUUAGAGGAUGAUCAGCCACACUGGAACUGAGAUACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCACAAUGGGCGAAAGCCUGAUGGAGCAAUACCGUGUGAGGGAUGAAGGCCUGUGGGUUGUAAACCUCUUUUUUCAGGAAAGAAACUUUGACGGUACCUGAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCACUGGGCGUAAAGCGUCUGUAGGUGGUUUAUCAAGUCUGCUGUUAAAGCUUGAGGCUUAACCUCAAAAAAGCAGUGGAAACUGAUAGACUAGAGAAUGGUAGGGGCAGAGAGAAUUCUCAGUGUAGCGGUGAAAUGCGUAGAUAUUGAGAAGAAUACCGAUAGCGAAGGCGCUCUGCUGGGCCAUUACUGACACUCAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGAUGUUGUGUGAGUAAAAUUGUGCAGUAUCGAAGCUAACGCGUUAAGUAUCCCGCCUGGGAAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGACUUGACAUGUUACUAAUUUCCUUGAAAGAGGAAAGUGCCUUUGGGAAAGUAAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUACCAUCAUUAAGUUGGGGACUCUAAAGAGACUGCCGGUGAUAAACCGGAGGAAGGUAAGGAUGAGGUCAAGUCAUCAUGCCCCUUAUGUCCUGGGCUACACACGUGCUACAAUGGUUAGGACAAUAAGUCGCAAAUUCGUGAGAACUAGCUAAUCUUAUAAACCUAAUCUCAGUACGGAUUGUAGGCUGCAACUCGCCUACAUGAAGACGGAAUCGCUAGUAAUCGCUGGUCAGCUACACAGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGGAGCUGGCCAUGUCCGAAAUCAUUACUCUAACCUUAAUGGAGGAGGAUGCUUAAGGCAGGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUUACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq new file mode 100644 index 0000000..b5a551f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.fragile.seq @@ -0,0 +1,2 @@ +>d.16.c.C.fragile +UUGAAAUGGAGAGGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGAUAUGCUUAACACAUGCAAGUCGAACGAAUAUUAAGUUUUCUUAAAUUUGUAGAAAUUUAAUAUUAGUGGCGAACGGGUGAGUAACGCGUAAGAAUCUGCUUUUGGGUAAAGAAUAACAAUUGGAAACGAUUGCUAAUACUUUAUAGGCUGAGGAGUUAAAGGUUUUAUUUCCGCCCAGAAAUGAGCUUGCGUCUGAUUAGCUAGUUGGUAAGAUAAAAGCUUACCAAGGCAAUGAUCAGUAGUUGGUCUGAGAGGAUGAUCAACCACACUGGGACUGAGAUACGGCCCAGACCUUUACGGAGGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUAUCGCGUGAAGGAUGACGGCCUGUGGGUUGUAAACUUCUUUUCUUAAGAAAGAAUUCUGACGGUACUUAAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGAAAUUAUUGGGCGUAAAGAGUUUGUAGGUGGUUUUUUAAGUCUACUGUUAAAUAUCAGAGCUUAACUUUGAACAAGCAGUAUGAAACUAAUUAACUUGAGUUUGGUAGAGGCAGAGGGAACUCUCGAUGUAGUGGUGAAAUACGUAGAUAUCGGGGGGAACACCAGUAGCGAAAGCGCUCUGCUGGGCCAUAACUGACACUGAGAAACGAAAGCUAGGGGAGCAAAUAGGAUUAGAUACCCUAGUAGUCCUAGCUGUAAACGAUGGAUACUAAGUAUUGGGCUUUUUGAAGUUCAGUGUUGAAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGAAUUGACAUACUCGUUGGUUUUUUAGAAAUAAAAAACUGUUAAAGAGAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUGUUAUCUAGAGAGACUGCCGGUGAUAAACCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUAAGUCCUGGGCGACACACGUGCUACAAUGGUAUAGACAAAGGGAAGCAAAUCUGCGAAGAGUAGCAAAUCUCAAAAACUAUAUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGCUGGUCAGCCAUACAGCGGUGAAUAUGUUCUCGGGCCUUGUACACACCGCCCAUCACGCUCGAGAAAUUGGAAAUACCCAAAGUCAUCAUUCUAACCAUAUUUUUUGGAAGAUAAUGCCAAAGGUAGAGCUAGUGACUCAAGCGAAGUUGUAACAAGGUAACCGUACUGGAAGGUGCGGUUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq new file mode 100644 index 0000000..665ca3f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.reinhardtii.seq @@ -0,0 +1,2 @@ +>d.16.c.C.reinhardtii +AUCCAUGGAGAGUUUGAUCCUGGCUCAGGACGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGAACGAGCAAAGCAAUUUGUGUAGUGGCGAACGGGUGCGUAACGCGUAAGAACCUACCUAUCGGAGGGGGAUAACAUUGGGAAACUGUUGCUAAUACCCCAUACAGCUGAGGAGUGAAAGGUGAAAAACCGCCGAUAGAGGGGCUUGCGUCUGAUUAGCUAGUUGGUGGGGGUAACGGCCUCCCAAGGCCACGAGCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUUCGCAAUGGGCGCAAGCGACGGAGCAAUGCCGCGUGCAGGAAGAAGGCCUGUGGGUCGUAAACUGCUUUUCUCAGAGAAGAAGUUCUGACGGUAUCUGAGGAAUAAGCACCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGGUGCAAGCGUUGUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUCGUAAAGUCUAAUGUCAAAUACCAGGGCUCAACCUUGGACCGGCAUUGGAGUACUCACGAGCUUGAGUACGGUAGGGGCAGAGGGAAUUCCAUGUGGAGCGGUGAAAUGCGUAGAGAUAUGGAGGAACACCAGUGGCGAAGGCGCUCUGCUGGGCCGAAACUGACACUGAGAGACGAAAGCUGGGGGAGCGAAUAGGAUUAGAUACCCUAGUAGUCCCAGCCGUAAACUAUGGAGACUAAGUGCUGCCGCAAGCAGUGCUGUAGCUAACGCGUUAAGUCUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGACCGCACAAGCGGUGGAUUAUGUGGAUUAAUUCGAUACAACGCGAAGAACCUUACCAGGGUUUGACAUGUCAAGAACCUCUCAGAAAUGGGAGGGUGCCCUAACGGACUUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCUGUGAAGUGUAUAGUUAAGUCUCAUAACGAGCGCAACCCUCGUCUUUAGUUGCCAUUUGGUUCUCUAAAGAGACUGCCAGUGUAAGCUGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACAUCCUGGGCUUCACACGUAAUACAAUGGUUGGGACAAUCAGAAGCGACUCGUGAGAGCUAGCGGCUCUGUUAAACCCAACCUCAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUGAAGCCGGAAUCGCUAGUAAUCGCCAGUCAGCUAUAUGGCGGUGAAUACGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUUCUGCUCCAAGUCGUUACCCUAACCUUCGGGAGGGGGGCGCCUAAAGCAGGGCUAGUGACUAGGGUGAAGUCGUAACAAGGUAGGGCUACUGGAAGGUGGCCCUGGCUCACCUCCUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq new file mode 100644 index 0000000..c5ee178 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.C.vulgaris.seq @@ -0,0 +1,2 @@ +>d.16.c.C.vulgaris +UGCCUGCAGAGAGUUYGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGUACGCAUGCAAUUUGGCUUGCCAGAUUGCGAUGAGUGGCGGACGGGUGAGUAACACGUAAGAACCUACCUUUUGGAGAGGGAUAACCAUUGGAAACGAUGGCUAAUACCUCGUAUUGCUGAGAAGUGAAAGAUGAAAAUCGCCAAUAGAUGGGCUUGCGGCUGAUUAGCUUGUUGGUGAGGUAAUGGCUUACCAAGGCAAUGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGACAGCCUGACGGAGCAAUGCCGCGUGAAGGAUGAAGGCCUAUGGGUUGUAAACUUCUUUUCUCAGAGAAGAAGCAUUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUAAAAAGUCUCCUGUCAAAGAUCAGGGCUUAACCCUGGGCCGGCAGGAGAAACUCUUAGGCUAGAGUUUGGUAGGGGCAGAGGGAAUUCCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGGAGGAACACCAAAGGCGAAAGCACUCUGCUGGGCCAUAACUGACACUGAGAGACGAAAGCGAGGGGAGCAAAAGGGAUUAGAUACCCCUGUAGUCCUCGCCGUAAACGAUGGAUACUAGAUGUUGGGUAGGUUAAAUCACUCAGUAUCGUAGCUAACGCGUGAAGUAUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGACUUGACAUGCCACUUUUUCCCUGAAAGGGGAAGUUCCAGAGUGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCUUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUUUGAAUUGCCAGUAAUGGGAAAUUCAAAAGACUGCCGGUGACAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACGUCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGAGAUGCAAACCCGCGAGGGCUAGCCAACCUCAAAAACCCGGUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUCGGAAUCGCUAGUAAUCGCAGGUCAGCCAUACUGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGCUGGCUAUGCCCAAAGUCGUUACCCCAACCUUUUAGGAGGGGGACGCCUAAGGCAGAGCUAGUGACUAGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGWGGYUGGAUCACCUCCUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq new file mode 100644 index 0000000..3b7fc1b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Cryptomonas.sp.seq @@ -0,0 +1,2 @@ +>d.16.c.Cryptomonas.sp +AAAUCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGUACGAAAGUUUUUAACUUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCCUUAGGAGGAGGGGGAUAACAGCUGGAAACGGCUGCUAAUACUCCAUAUGCUGAAGAGUGAAAGGGAAACCACCUAAGGAAGAGCUCGCGUCUGAUUAGCUAGUUGGUAGGGUAAGGGCCUACCAAGGCGACGAUCAGUAGCUGGUUUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGCAAGCCUGACGGAGCAAUACCGCGUGAGGGAUGAAGGCCUGUGGGUUGUAAACCUCUUUUCUCAAGGAAGAAGUUCUGACGGUACUUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAUACAGAGGAUGCAAGCGUUAUCCGGAAUUACUGGGCAUAAAGCGUCUGUAGGUUGUUUAGUAAGUCUGCUGUUAAAGACUAGGGCUUAACCCUAGAAAAGCAGUGGAAACUGCUAGACUUGAGUGUGGUAGAGGUAGAGGGAAUUCCUAGUGUAGCGGUGAAAUGCGUAGAUAUUAGGAAGAACACCAAUGGCGAAAGCACUUUACUGGGCCAUAACUGACACUGAGAGACGACAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGAUGUUGUACGUAUUAACCCGUACAGUAUCGUAGCUAAGGCGUUAAGUAUCCCGCCUGGGAAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUGUCACAAAUUUUCUUGAAAAAGAAAAGUGCCUUCGGGAAUGUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGUAACCCUUGUUUUUAGUUGCCAUCAUUAAGUUGGGCACUUUAAAAAGACUGCCGGUGAUAAACCGGAGGAAGGUGAGGACGACGUCAAGUCAGCAUGCCCCUUACACUCUGGGCUACACACGUACUACAAUGGUCGAGACAAAAAGUCGCAAACUUGUGAAAGUAAGCUAAUCUUAUAAACUCGAUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUAGUCAUACCCAAAGUCGUUACCUUAACCAUUCGGAGGGGGGCGCCUAAGGUAGGGUUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq new file mode 100644 index 0000000..6c04b9e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.E.gracilis.seq @@ -0,0 +1,2 @@ +>d.16.c.E.gracilis +UGGAAAUGACGAGUUUGAUCCUUGCUCAGGGUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUUGAACGAAAUUACUAGCAAUAGUAAUUUAGUGGCGGACGGGUGAGUAAUAUGUAAGAAUCUGCGCUUGGGCGAGGAAUAACAGAUGGAAACGUUUGCUAAUGCCUCAUAAUUUACUAGAUCUAUGUGAGUAGCUAGUUAAAGAGAAUUUCGCCUAGGCAUGAGCUUGCAUCUGAUUAGCUUGUUGGUGAGGUAAAGGCUUACCAAGGCGACGAUCAGUAGCUGAUUUGAGAGGAUGAUCAGCCACACUGGGAUUGAGAACGGAACAGACUUCUACGGAAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGCAAGCCUGACGGAGCAAUACCGCGUGAAGGAAGACGGCCUUUGGGUUGAAAACCUCUUUUCUCAAAGAAGAAGAAAUGACGGUAUUUGAGGAAUAAGCAUCGGCUAAUUCCGUGCCAGCAGCCGCGGUAAUACGGGAGAUGCGAGCGUUAUCCGGAAUUAUUGGGCGUAAAGAGUUUGUAGGCGGUCAAGUGUGUUUAAUGUUAAAAGUCAAAGCUUAACUUUGGAAGGGCAUUAAAAACUGCUAGACUUGAGUAUGGUAGGGGUGAAGGGAAUUUCCAGUGUAGCGGUGAAAUGCGUAGAGAUUGGAAAGAACACCAAUGGCGAAGGCACUUUUCUAGGCCAAUACUGACGCUGAGAAACGAAAGCUGAGGGAGCAAACAGGAUUAGAUACCCUGUAGUCUUGGCCGUAAACUAUGGAUACUAAGUGGUGCUGAAAGUGCACUGCUGUAGUUAACACGUUAAGUAUCCCGCCUGGGGAGUACGCUUGCACAAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACACGAAGAACCUUACCAGGAUUUGACAGGAUCUAGGAAGUUUGAAAGAACGCAGUACCUUCGGGUAUCUAGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUUUUUAAUUAACGCUUGUCAUUUAGAAAUACUGCUGGUUAUUACCGGAGGAAGGUGAGGACGACGUCAAGUCAUCAUGCCCCUUAUAUCCUGGGCUACACACGUGCUACAAUGGUUAAGACAAUAAGUUGCAAUUUUGUGAAAAUGAGCUAAUCUUAAAACUUAGCCUAAGUUCGGAUUGUAGGCUGAAACUCGCCUACAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUACGUUCUCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGUCGGCUGUGCCCGAAGUUAUUAUCUUGCCUGAAAAGAGGGAAAUACCUAAGGCCUGGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGUGGCUGGAACAACUCC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq new file mode 100644 index 0000000..13a55b3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.africana.seq @@ -0,0 +1,2 @@ +>d.16.c.H.africana +UCUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUUGAACGAGAAAUAGAACAACUAUUUCUAGUAGCGAACGGGUGCGUAAUUACAUAAGAACUUAUCCUUUUAAGAAGGAAAUAACAAAUAACAAAUGGAAACAUUUGCUAAUGUCCUAUAAGCUGAAAAGUAAAAGGAUUAAAUCCACUAAAGGUAAGGCUUAUGUCUAGUUAGUUGGUAAGGUAACAGCUUAACAAGACAAUGAUCAGUAAUUGGUCUGAGAGGAUGAUCAAUCACACUGGAACUGAGAUAAGGUCCAGACUCCUACGGGUGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCUGACGGGGCAAUGUUGCGUGAAGGCAGAAGGCCGAUAGGUUGUAAACUUCUUUUGUGAGAAAAUAAGGAAAAUGACAGUAUCUCAAGAAUAAGCAUCGGCUAACUUUGUGCCAGCAGCCGCGGUGAUACAGAGGAUGCGAGCAUUAUCCGGAAUUAUUGGGCGUAAAGUGUUUUAAGGUGGCUUUAUAAGUCUAUCGUUAAAUCUCAGAGCUUAACUCUGAUUAGGCGAUUGACUAUUAAGCUAGAGCUUUGAAUAAAGCAAGGGGAAUUUCUAAUGAAGCGGUUAAAUGCGUUGAGAUUGGAAAGAACACCAAGGGCGAAAGCACUCUGCUGGGCCAAAAUUGACACUGAUAAACGAAAGCUAGGGUAGCGAGAGGGAUUAGACACCCCAAUAGUCCUAGCUGUAAACAAUGGAUACUUAGCAUUACUAUAUGAAAAGAUAGCUAAGCUUAAAGCUAACGCAAUAAGUAUCCCGCCUGGGAAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGGCGGGGGUUCACGCAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUACCAGGGAUUGUAUGUCGUAAUCUUUCUGAAAAAGUAAGAUACGUAUUUAUUUAAUAAAUAAAUACGUAGACACAGGUGGUGCAUGGCUGUCGUCAGCCCGUGCUGUCAAGCGUAGGGUUAACUCCCAUAACGGGCGCAACUCCCAUGUUUAGUUACCAAUUUAUGGUACUCUAAACAAACAGCUAAUGAUAAAUACUAAAUUAGAGGAAGGUGGGGAAGACGUCAAGUCAUCAUGCCCUUUAUACUCUGGGCUACACGCGUGCUACAAUGGCUGGGACAAAAUGUUGCAAUUCUGUAAAGAUAUAGCAAAACAUAAAACCCAGUCUCAGUUCGGAUUCGGGCUGCAACUCGCCCGCAUGAAGUCGGAAUCGCUAGUAAUCGCUGGUCAGCAAUACAGCGGUGAAUAAGUCACCGGACCUUGUACACACCGCCCGUCACACUCAGGAAAUUGGUCAUGCCCUAACUCAUUUUAAUAUAAUGAUAAAGGUGAGGCUGGUAACUAGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq new file mode 100644 index 0000000..7f1d3dd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.H.akashiwo.seq @@ -0,0 +1,2 @@ +>d.16.c.H.akashiwo +UUUUAGGAUAUAAUUGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAGAGGUUUUUAAAGAUUUUUCUUAAAAAACUGAAAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUGCCUUUAGGAAAGGGACAACAUUUGGAAACGAAUGCUAAUACCUUAUAUGCCUAUUAUAACUUGUAUAAUUAAUAGGUGAAAAGUUUUCUGCCUAGAGAGGAGCUCGCGGCUGAUUAGCUAGUUGGUGGGGUAAUGGCCUACCAAGGCGACGAUCAGUAACUGAUUUGAGAGGAUGAUCAGUCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCUGCAAUGGGCGAAAGCCUGACAGAGCAAUACCGCGUGAGGGAUGACAGUCCUAUGGAUUGUAAACCUCUUUUUUCAGGGAGGAAGUUCUGACGUUACCUGAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGUGUUAUCCGGAAUCACUGGGCGUAAAGCGUCUGUAGGUGGUUUAAUGUGUCUGUUGUUAAAUCUUAAGGCUCAACCUUAAACCAGCAAUGGAAACUAUUAUGACUUGAGUGUGGUAGAGGUAGAGGGAAUUUCCAGUGGAGCGGUGAAAUGCGUAGAUAUUGGAAAGACCACCAAUGGCGAAGGCACUCUACUGGGCCAUUACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCUGUAAACGAUGGAUACUAGAUGUCGCAUGUAUCGACCCAUGCGGUAUUAUAGCUAACGCGUUAAGUAUCCCGCCUGGGAAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUAGUACGAAGUUUUUUGAAAAAAAAACCACCUUCGGGAACGUACAUACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGUAACCCUUGUUUUUAGUUGCCUUUCGAGGAUAUUUAGAAAGACUGCCGAUUAUAAAUCGGAGGAAGGUAAGGACGACGUCAAGUCAUCAUGCCCCUUACACUCUGGGCUACACACGUGCUACAUUGGGUAGAACAAUAAGUUGCUAAGUUGCGAAACCAAGCGAAUCUUCAAAUCUACUCUAAGUUCGGAUUGUAGGCUGCAACUCGCCUACAUAAAGAUGGAAUCGCUAGUAAUCGCUGGUCAGCUACACAGCGGUGAAUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUCACACCCAAAGUCGUUAUUCUAACCGUUUGGAGGAAGGCGCCUAAGGUAGGAUUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACCGGAAGGUGCGGCUGGAUCACCUCCUUAUAAAGGUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq new file mode 100644 index 0000000..516122e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.M.polymorpha.seq @@ -0,0 +1,2 @@ +>d.16.c.M.polymorpha +UCUCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGUACGGGAAGGAUCCUAGUGGUGUUUCCAGUGGCGGACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGGACAACAGCUGGAAACGGUUGCUAAUACCCCAUAGGCUGAGGAGCAAAAGGAGGAAUCCGCCUAAGGAGGGGCUUGCGUCUGAUUAGCUAGUUGGUGAGGUAAUAGCUUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCUUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAACGUGACGGAGCAAUGCCGCGUGGAGGUAGAAGGCUCACGGGUCGUAAACUCCUUUUCUCAGAGAAGAUGCAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUUAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGAAAGAACACCAAUGGCGAAAGCACUCUUCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAAGCGCUGUGCUAUCGACCCGUGCAGUGCUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCCGUGAAUCUUUUUGAAAGAAAAGAGUGCCUUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCUUGUUUAGUUGCCAUCAUUAAGUUUGGAACCCUAAACAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUACGCCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGGGUCGCGACCUCGCGAGAGAAAGCUAACCUCAAAAACCCGGCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUGGGAGCUGGCCAUGCCCGAAGUCGUUACUCUAACCGUAAGGAGGGGGGUGCCGAACAGGGGCUAGUGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq new file mode 100644 index 0000000..09f3dac --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.falciparum.seq @@ -0,0 +1,2 @@ +>d.16.c.P.falciparum +UUAUAUUGCGAGUUUGAUCCUAGCUCAGAAUUAACGCUAGAAAUAUACAUUACACAUGCAAAUUAAUGAUAAUAUCAUAGUGUAUAGGUGAGGAUAUAUAAAUUUUUAAUUUUAAAUAGAUUAUAAAUUUUAUUAAAUAAUAAUCUAUAAGCGCAAAAAUAUAUGUACUAUAUUAAAAAUUAAUAUUAUUUAAAAUAAAAUUUAUAUUUGAUUAACUAGUUGGUAAUUUAAAAGACUACCAAGGUUAUUAUCAAAAAUUGGUUUGAAAGAAUGUACAAUCACAUUAGGAUUGAAAUAAAGCCUAAAUUUUUAUAAAAAAUCAGCAGUGAGGAAUAUUUUACAAUAAGUGUAAGCUUGAUAAAGUAAUAUUUCUUUUAGGAAGACAGUAUUAUUAAAAUAUUGUAAACUUUUUAUUUUAUUUUUAAAUAUUGAUAAAAAUAAAAAAUAGUAUUUGCUAUUUCUGUGCCAGCAGCAGCGGUAAUACAGAAAAUGCAAGCGUUAUUCAUUUUAUUAGGCGUAAAGCGUUUUAAGGUUUUAUAUUAAUUUUAUGUUUAAAUAUUUAAAUUAAAUUUAAAAUAAAUUAAUAAAUAAUAAUAUAAUAGAGUAUUAUAAAAGUAUUAAGAAUUUUUUGAGAAGUAGUGAAAUACAAUGAUACAAAAAAGAAUAUCAAAGGCGGAAGCAUAAUACUAUAUAAUUACUGACACUUAAAAACGAAAGCUAAGGUAGCAAAUAGGAUUAGAUACCCUAGUAGUCUUAGCUGUAAACUAUGAAUAUUUUAUAUUUAUAUUUUAUAAAUAUAAUAACUAACGUGAUAAAUAUUCCGCCUGAGUAGUAUAUUCGCAAGAAUGAAAUUCAAAGGAAUUGACGGGAGCUUAUACAAGUGGUGGAACAUGUGGCUUAAUUCGAUGCAACACGAUAAACCUUACCAAAAUUUAACAAUAUUUUUAAUAUUAAGAAAUUAAUAUUUUAAUAAAAUAUAUAGGUAGUGCAUGGCUGUCGUCAGUUCGUGCUGUGAAGUGUUAAUUUUAGUAUUAUAACGAACGUAACCUUUUAUAAAAAAAAUUUUUAUAAUAAAUAAUAAUAAAGAUUACGUCAAGUCAUUAUGCUCCUUAUAUUUUGGGCUGCUCACGUGUUACAUAAAAUAUUACAAUAUUUUAUUAUAUGUUAAAUAUAAUAAUUAAAAUAUAUUUAUAGUUCAGAUUAUAAAUUGAAACUCAUUUAUAUAAAGAUGGAAUCACUAGUAAUCGCUAAUCAGAAUUAUAGCGGUGAAUAAGUUCUUAAGCUUUGUACACACCGCCCGUCACAUCUAAAAAGUAUCAUAUUAUAUAAAAAUUAUUGUUAAAUAAUAAUAUAUAAUUAUAUAAUUUAGAUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUAAUAAAAUAAAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq new file mode 100644 index 0000000..6a92f4d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.littoralis.seq @@ -0,0 +1,2 @@ +>d.16.c.P.littoralis +AAACUAUCGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUUACACAUGCAAGUCGUACGAAAGUGUUAAAACUUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUUUACCUUUAGGAGGGGAAUAACAGUUGGAAAUGACUGCUAAUGCCGCAUAUCGUAAUUAUGAGACAUAUCAUAACUAUGAAAGAAGAAAUUCGCCUAAAGAAAAGCUUGCGUCUGAUUAGCUAGUUGGUAAGGGUAAAGGCUACAAGGCGACGAUCAGUAGCUGGUUUGAGAGGACGACCAGUCACACUGGACUGAGACACGGUCCAGACUACUACGGGAGGCAGCAGUGGGGAAUUUUCUGCAAUGGGCGAAACUGAACAGAGCAAUACCGCGUGAGGGAAGAAAGCCCACAGGGUUGUAAACCUCUUUUGUCAAGGAAGAAGAUUCUGACGUUACUUGACGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGGACGGGGGAUGCAAGUGUUAUCCGGAAUUACUGGGCGUAAAGCGUUUGUAGGUGGUUUAGUAAGUCUAUUGUUAAAGCUUGAAGCUUAACUUCAAAAGUGUAAUAGAAACUACUAGACUUGAGGAUAGUAGGGGUAAAGGGAAUUUCCAGUGGAGCGGUGAAAUGCGUAGAGAUUGGAAGGACCACCGAUGGCGAAGGCACUUUACUGGGCUAUUUCUGACACUAAGAGACGAAAGCUAGGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCUGUAAACGAUGAAUACUAGAUGUUGCGUGUAUCGAUCCAUGCAGUAUCGUAGCUAACGCGUUAAGUAUUCCGCCUGGGAACUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGACCCGCACAAGCGUGGCAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUUAUGUAAAUCUAUUUGAAAGAACAGAGUGCCCUCGGGAAUACAUAAACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUUUCUAGUUGCUUUACAAAAGGAAUCUUGAAGACUGCCGGUUAUAAACCGGAGGAAGGUGAGGAUGACGUCAAGUCAUCAUGCCCCUUAUACCCUGGGCUACACACGUGCUACAUUGGAUAAGACAAAAAGUUGCGAAUUUGUGAAAAUAAGCUAAUCUUUAAACUUAUUCCUAAGUUCGGAUUGAAGGCUGCAACUCGCCUUCAUGAAGAUGGAAUCGCUAGUAAUCGCUGGUCAGCUAUACAGCGGUGAAUCCGUUCCCGGGUCUUGUACACACCGCCCGUCACACCAUGGAAGCUGGUUAUACCCGAAGUCGUUUUCUUAACCUUUUUGGAGAGAGGCGCCUAAGGUAAGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACGGGAACGUGCGGCUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq new file mode 100644 index 0000000..42ff17e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.minor.seq @@ -0,0 +1,2 @@ +>d.16.c.P.minor +AUUUUUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCCUAACACAUGCAAGUCGAACUAGCUCUAGCGCAAGUUAGAGUGGGUGGCGGACGGGUGAGGAACACGUAAGAACCUACCCUUUGGAGGAGGAUAACUGUUGGAAACGGCAGCUAAUACUCCAUAUGCUGAGGAGUAAAAGGUCGAAAGGCCGCCAAGGGAUGGGCUUGCGUCUGAUUAGCUAGUUGGUGAGGUAAAUGCUUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAAGGAUGAAGGCCUGUGGGUUGUAAACUUCUUUUCUCAGAGACGAAUAAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUCCAAGUCUUUUGUCAAAUCCCAGAGCUUAACUUUGGAUCGGCACGAGAAACUCGAGAGCUUGAGUAUGGUAGGGGCAGAGGGAAUUCCCGGUGUAGCGGUGAAAUGCGUAGAGAUCGGGAAGAACACCGAUGGCGAAAGCACUCUGCUGGGCCAUUACUGACACUGAGAGACGAAAGCUAAGGGAGCGAAUAGGAUUAGAUACCCUAGUAGUCUUAGCCGUAAACGAUGGAAACUAAGUGCUUGGGCCGCGAGUAAUCGCUGCUUGAGUCCUGUAGCUAACGCGUUAAGUUUCCCGCCUGGGAAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGCUUGACAUGCCACUCUUUCGGGAGGUCAUGGUGAAAGCCAGUUUAGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUCUUGUUGCAACUUUGUUGUUAUCGAGAGAGACUGCCGGUGAUAAGUCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUACGCCCUGGGCAACACACGUGCUACAAUGGCCAGGACAAAGAGAUGCAACCUCGCAAGAGCAAGCCAACCUCAAAAACCUGGUCUCAGUUCGGAUUAGUCUCUGCAACCCGAGACUAUGAAGCCGGAAUCGCUAGUAAUCGCUGGUCAGCUAUACAGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGGAGCUGGCUAUGCCCAAAGUCGUUACCCCAACCGUUUGGAGGGGGAUGCCUAAGGCAGAGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq new file mode 100644 index 0000000..69f34fd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.palmata.seq @@ -0,0 +1,2 @@ +>d.16.c.P.palmata +ACACCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAAGGUUUUACCUUAGUGGCGGACGGGUGAGUAACACGUGAGAAUCUACCCUUGGGAGGGGAAUAACAGUUGGAAACGAUUGCUAAUGCCCCAUAAGCUGAAAAGUAAAAUGAUUUUUCGCCCAGGGAUGAGCUCGCGCCUGAUUAGCUAGUUGGUAAGAUAAAAGCUUACCAAGGCAACGAUCAGUAGCUGGUUUGAGAGGACGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUUCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCUGACGGAGCAAUACCGCGUGAGGGAAGAAUGCCCGUGCGUUGUAAACCUCUUUUCUUAGGGAAGAAGCUCUGACGGUACCUAAAGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCACUGGGCGUAAAGUGUAGUAGGUGGCUUAUAAAGUCCGCUGUUAAAUCUUAGGGCUCAACCCUAAGCCAGCAGUAGAAACUUCUAGGCUAGAGUAUGGUAGGGGCAGAGGGAAUUCCCAGUGUAGCGGUGAAAUGCGUAGAUAUUGGGAAGAACACCAGAGGCGAAAGCGCUCUGCUAGGCCAUUACUGACACUCAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGAUGUUGCGCGUAUCGAUCCGUGCAGUAUCGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGAGCUUGACAUGUCACGAAUUUUUUCGAGAGAAAAAAGUGCCUUAGGGAACGUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUGUCUUUAGUUGCCAUCAUUUAGUUGGGCACUCUAGAGAGACUGCCGGUGACAAACCGGAGGAAGGUAAGGAUGACGUCAAGUCAGCAUGCCCCUUACGCUCUGGGCUACACACGUGCUACAAUGGUCGCGACAAAGAGUUGCCAGUCUGCAAAGACGCGCUAAUCUCAUAAACGUGGCCUCAGUUCGGAUUGUAGGCUGAAACUCGCCUACAUGAAGGUGGAAUCGCUAGUAAUCGCCGGUCAGCUACACGGCGGUGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGAAGCUGGCCACGCCCAAAGUCGUUACCCUAACCUUUUGGAGGGGGGCGCCUAAGGCAGGGCUAGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq new file mode 100644 index 0000000..6ae32f5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.P.wickerhamii.seq @@ -0,0 +1,2 @@ +>d.16.c.P.wickerhamii +UGUGAAAACGAAGAGUUUGAUCCUGGCUCAGGAUAAACGCUGGCGGCAUGCUUAACACAUGCAAGUUGUACGAAGGUAUUUAUCUUUCGAGCUAAAUAUACUGAGUAGCGGACGGGUGAGUAACACGUAAGAAUCUACCUUUUGGAGAGGGAUAACUACUGGAAACGGUAGCUAAUACCUUAUAUUGCUGAGAAGUGAAAAAUGUAAAUUGCCAGAAGAUGAGCUUGCGCCUGAUUAGCUAGUUGGUGUGGUAACUGCAUACCAAGGCAAUGAUCAGUAGCUGUUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGAGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGAAGGAUGACGGCCUAUGGGUUGUAAACUUCUUUUCUCAGAAAAGAUUAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUUGUUUAAAAAGUAUUCUGUCAAAAAUUAGGGCUUAACCCUAUACAGGCAGAAUAAACUUUUAAGCUAGAGUUUGGUAGAGGCAGAGGGAAUUCCCGGUGGAGCGGUGAAAUGCGUAGAUAUCGGGAGGAACACCAAAGGCGAAGGCACUCUGCUGGGCCAAUACUGACACUGAGAGACGAAAGCGAGGGGAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUCGCUGUAAACGAUGGAUACUAGGUGUUGGGUGUAUCAAAAACAUUCAGUAUCGUAGCUAACGCAUUAAGUUUCCCGCCUGGGGAGUAUGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGAACCCGCACAAUUGGUGGGGUACGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGAUUUGACAUGUCAUUUGUUUCUUCAACUUAAUACUUUAAUUUGUUUUAAGUAGAAACAUAAAAAAAUGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCUUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUUUUUUUGAAUUGCUUGGGGCAUUAUAUGCCUUUUUACAGAGGAAAUUCAAAAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAGCAUGCCCCUUAUAUCCUGGGCGACACACGUGCUACAAUGGACGUAACAAAGAGAAGCUACUUCGCGAGAACAAGCUAAUCUCAAAAAUACGUUCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGUUGGAAUCAAUAGUAAUCGCAGGUCAGCCACACUGCGGUGAAUACGUUUCCGGGUUUUGCACACACCGCCCGUCACACCACGGAAAUUGGCUACGCCCUAAAUCAUUACCCUAACCAUUCUGUGGAGGGGGAUGCCUAAGGCGGGGCUGGUAACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq new file mode 100644 index 0000000..8de7320 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.S.oleracea.seq @@ -0,0 +1,2 @@ +>d.16.c.S.oleracea +UCUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGGACGGGAAGUGGUGUUUCCAGUGGCGGACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGAACAACAGCUGGAAACGGCUGCUAAUACCCCGUAGGCUGAGAAGCAAAAGGAGGAAUCCGCCCGAGGAGGGGCUCGCGUCUGAUUAGCUAGUUGGUGAGGUAAUAGCUUACCAAGGCGAUGAUCAGUAGCUGGUCCGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGGAGGCAGAAGGCCCACGGGUCGUGAACUUCUUUUCCCGGAGAAGAAGCAAUGACGGUAUCCGGGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUUAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCGUAGAGAUCGGAAAGAACACCAACGGCGAAAGCACUCUGCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCGAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGCGCUGUGCGUAUCGACCCGUGCAGUGUUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAAGCGAAGAACCUUACCAGGGCUUGACAUGCCGCGAAUCCUCUUGAAAGAGAGGGGUGCCUUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUGUUUAGUUGCCAACGUUGAGUUUGGAACCCUGAACAGACUGCCGGUGAUAAGCCGGAGGAAGGUGAGGAUGACGUCAAGUCAUCAUGCCCCUUAUGCCCUGGGCGACACACGUGCUACAAUGGCCGGGACAAAGGGUCGCGAUCCCGCGAGGGUGAGCUAACCCCAAAAACCCGUCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCCGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUGGGAGCUGGCCAUGCCCGAAGUCGUUACCUUAACCGCAAGGAGGGGGAUGCCGAAGGCAGGGCUAGUGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq new file mode 100644 index 0000000..b37e535 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.T.gondii.seq @@ -0,0 +1,2 @@ +>d.16.c.T.gondii +AAAUUAUUACGAGUUUGAUCCUGGCUCCGGAAGAACGCAAGAGAUGUGCUUAACACAUGCUAAUUGAAUGGUAUUAAUAUAUCAUAGUGUAAUAGUGAGUAAUGUAUGAGAAUUUAUUUUUAGAAUAUAAUAAAAAUUUAAUAAUUUAUAAUAAACGCAAUAGUGUUUUAAAAGAUAAUUAUUGUCUAAAAAAAAGCUCAUAUCUAAUUAGCUAGUUGGUGAAGUAAUAGUUUUACCAAGGCGAAGAUUAGUAGCUGCCUUGAGAGGGGAAACAGCCACAUAGAGAUUGAAAUACAGCUCUAACUCCUAAGGGGGGCAGCAGUGGGGAAUUUUCUGCCAAUAAGCGCAAGCUUGACAGAGCGUCAUCACAUGAAGGAGGAAGGCCUAUAAAGGUUGUAAACUUCUUUUGCUUAAAAAAAUAAUACUGACGUUUAAGUUUAAAAAGUAUCGGCUAACUCCGUGCCAGCAGCCGCGGUCAUACGGGGGAUACAAGCGUUUUCCAAAAUUACUGGGCGUAAAGUGUAUGUAGGUGGAUUGGUAUGUUCUUCCUUAAAUACUAUUUGAUAAAUUUAGAAAAAGGAAGAAAACUAUUAAUCUUGAGUUCGAUAAGGGUAAGAGGAAUUUUUUGAGGAGUAGUGAAAUGCGAAGAUACAAAAAAGAAGAUCAACAGCGAAAGCAUCUUACUGGGUCGAUACUGACACUGAGAUACGAAAGUUAAGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCUUAACUGUAAACAAUGGAUACUCGGUACUGGAGACAUUAAAUAUAUAAAUUCAGUACCCUAGCUAACGCGUUAAGUAUUCCGCCUGAGUAGUACGCUCGCAAGGGUGAAACUCAAAGGAAUUGACGGGGGCUCGUACAAGCGGUGGAGCACGUAAUUUAAUUCGAUGUAACGCGAUAAACCUUACCAGAACUAGACUAAAUUUAUUUUAAAUUAUUAAUAUUAAUUAAUAAAAAAUUUACAGGAGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCUACGAGCGCUACCCUUAUUUAAAGUUUUUUAUAUCUUUAAAAACAGACUAUAUAAAUUUUUGUACUAAAUUAGUAGGAAGGAGAGGAAAACGUCAAGUCUUUAUGCCCUUUAUGUUCUGGGCUACAUACGUGCUACAAUAGAUGGUACAAUAAUUUUUAAAAAUAAAUACAAUAUCAAUUUAUUUUUAAUUUAUUUGUGAAAAUAAAUGUAAUAAUUGAAAACCAUUUUUAGUUCGGAACAUAAACUGCAAUUUGUUUAUGUAAAGUUGGAAUCGCUAGUAAUCGCCGGUCAGCAUUACGGCGGUGAAUAAGUCUUCGAGCCUUGUACACACCGCCCGUCACGCCACGGAAAUUGAUUAUUUUUUAAAACUUUUGAUAAAAGGAUAAAUAAUAAUAAAUAACUGGGGUGAAGUCGUAACAAGGUAGCUGUACUGGAAGGUGCUGCUGGAUAAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq new file mode 100644 index 0000000..9bffa4d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.c.Z.mays.seq @@ -0,0 +1,2 @@ +>d.16.c.Z.mays +CUCAUGGAGAGUUCGAUCCUGGCUCAGGAUGAACGCUGGCGGCAUGCUUAACACAUGCAAGUCGAACGGGAAGUGGUGUUUCCAGUGGCGAACGGGUGAGUAACGCGUAAGAACCUGCCCUUGGGAGGGGAACAACAACUGGAAACGGUUGCUAAUACCCCGUAGGCUGAGGAGCAAAAGGAGAAAUCCGCCCAAGGAGGGGCUCGCGUCUGAUUAGCUAGUUGGUGAGGCAAUAGCUUACCAAGGCGAUGAUCAGUAGCUGGUCCGAGAGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUGCCGCGUGGAGGUGGAAGGCCUACGGGUCGUCAACUUCUUUUCUCGGAGAAGAAACAAUGACGGUAUCUGAGGAAUAAGCAUCGGCUAACUCUGUGCCAGCAGCCGCGGUAAGACAGAGGAUGCAAGCGUUAUCCGGAAUGAUUGGGCGUAAAGCGUCUGUAGGUGGCUUUUCAAGUCCGCCGUCAAAUCCCAGGGCUCAACCCUGGACAGGCGGUGGAAACUACCAAGCUGGAGUACGGUAGGGGCAGAGGGAAUUUCCGGUGGAGCGGUGAAAUGCAUUGAGAUCGGAAAGAACACCAACGGCGAAAGCACUCUGCUGGGCCGACACUGACACUGAGAGACGAAAGCUAGGGGAGCAAAUGGGAUUAGAGACCCCAGUAGUCCUAGCCGUAAACGAUGGAUACUAGGUGCUGUGCGACUCGACCCGUGCAGUGCUGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGUUCGCAAGAAUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAAGGCGAAGAACCUUACCAGGGCUUGACAUGCCGCGAAUCCUCUUGAAAGAGAGGGGUGCCCUCGGGAACGCGGACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGCCGUAAGGUGUUGGGUUAAGUCUCGCAACGAGCGCAACCCUCGUGUUUAGUUGCCACUAUGAGUUUGGAACCCUGAACAGACCGCCGGUGUUAAGCCGGAGGAAGGAGAGGAUGAGGCCAAGUCAUCAUGCCCCUUAUGCCCUGGGCGACACACGUGCUACAAUGGGCGGGACAAAGGGUCGCGAUCUCGCGAGGGUGAGCUAACUCCAAAAACCCGUCCUCAGUUCGGAUUGCAGGCUGCAACUCGCCUGCAUGAAGCAGGAAUCGCUAGUAAUCGCCGGUCAGCCAUACGGCGGCGAAUCCGUUCCCGGGCCUUGUACACACCGCCCGUCACACUAUAGGAGCUGGCCAGGUUUGAAGUCAUUACCCUUAACCGUAAGGAGGGGGAUGCCUAAGGCUAGGCUUGCGACUGGAGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq new file mode 100644 index 0000000..53be3ef --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ambigua.seq @@ -0,0 +1,2 @@ +>d.16.e.A.ambigua +NAACCUGGUUGAUCCUGCCAGUAGUGAUACGCUGUCAUUAAGACUAAGCCAUGCAUGUGUAAGUAUAAGAAGUACUCGAGACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAGAUCCGACUUCGGGAGGAUUGUAUUUAUUAGGUUACAAAACCAACCCUCUCUCGGGAGGUUCUUUGGGUGAGUCAUGAUAAGCAUGCGGAUCGCAGGGCUUUACGCCGGCGACGGAUCAUGUAAGUUCCUGCCCUAUCAGCUUCGGAUGGUAGGGUAUUGGCCUACCAUGGCAUUAACGGGUAACGGGAGAUCAGGGUUUGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACGAUAAAUAACAAUGCCGGGCCUUUCUAGGUCUGGCAAUUGGAAUGAGAACGAUGCAAASACCCUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCUGGUGGAGUCGGUCUGUCCUUCACUUGGUGUUGGUACGUGACUGUAUCUCUGCCCUCCUUGGUUGGAUCCAGUGCUGGCAUUUGGUUGUCGGUCUGGGGACGGCCAUCGUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCUUAGGCCUUGAAUACAUUAGCAUGGAAUAAUGAAAUAGGGUUUUGGCACUAUUUCGUUGGUUUGCGCGCCGAAACAAUGAUUAAUAGGGACAGUUUGGGGAUAUUCCUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACGACUGCGAAAGCAUUUAUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACCAUGCCGACUAGGGAUUUGCGGUUGUUCUUGUAGACUCCGUAAGCACCUUAUGAGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGBGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUCCGGUGAAUGAGUUUUCAUUGACCUGGUCUUCUUAGAGGGACUUUCGGUGACUAACCGAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGAUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUCUAGAACCUUGGCCGAGAGGCCUGGGUAAUCUUGUGAACGUGCAUCGUGAUAGGGAUUGAAUAUUGCAAUUAUUAUUCAUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGCGGUCCGUUCCUUUACUGGGAUGUGGCUGUGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq new file mode 100644 index 0000000..6dbbac3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.baicalensis.seq @@ -0,0 +1,2 @@ +>d.16.e.A.baicalensis +NAACCUGGUUGAUCCUGCCAGUAGUGAUACGCUGUCAUUAAGGACUAAGCCAUGCAUGUGUAAGUAUAAGAACUUUCGAGACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAGAUCCGACUUCGGGAGGAUCGUAUUUAUUAGGUUACAAAACCAACCCUCUUUCGGGAGGUUCUCUGGGUGAGUCAUGAUAAGCAUGCGGAUCGCACGGCUUUAUGCCGGCGUCGGAUCAGGUAAGUUCCUGCCCCAUCAGCUUCGGAUGGUAGAGUAUUGGCCUACCAUGGCGUUAACGGGUAACGGGAGAUCAGGGUUUGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACGAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACGAUGCAAAUACCCUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCUGGUGGAGUCGGUCUGUCCUUCACUUGGUGUUGGUUCGUGACUGUAUCUCUGCCCUCCUUGGUUGGAGCCAGUGUUGGCAUUCAGUUGUUGGGCUGGGGACAAUCAUCGUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCUUAGGCCUUGAAUACAUUAGCAUGGAAUAAUGAAAUAGGGUUUUGGCACUAUUUUGUUGGUUUGCGCGCCAAAAUAAUGAUUAACAGGGACAGUUUGGGGAUAUUCGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACGACUGCGAAAGCAUUUAUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUUGCGGUUGUUCUUGUAGACUCCGUAAGCACCUUAUGAGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACAGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUCCGGUGAAUGAGUUUUCAUUGACCUGGUCUUCUUAGAGGGACUUUCGGUGACUAACCGAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGAUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUCUAGAACCUUGGCCGUGAGGCCUGGGUAAUCUUAUGAACGUGCAUCGUGCUAGGGAUUGAAUAUUGCAAUUAUUAUUCAUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGGUCCGUUCCUUCAGUGGGAUGUGGCUGUGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq new file mode 100644 index 0000000..bd0b78d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bongranii.seq @@ -0,0 +1,2 @@ +>d.16.e.A.bongranii +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAACUCUUUUACUUGAAAACUGCGAACGGCUCAUUAUAUCAGUUAUAGUUUAUUGGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCGAUACCCUUCUGGGGUAGUAUUUAUUAGAUAGAAACCAACCCCUUCGGGGUGAUGUGGUGAUUCAUAAUAAGUUUACGAAUCGCAUGCCUUCGGGCGGCGAUGGAUCUUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGGAAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUGACACAGAGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUGUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUGUGGCUGUUGCGGGAGGCCUGGCACGUGCCAGCGCUCUUCCUGCGACGCCAUCCUUGGGUUGAAAGUGGGUGGCAUUAGGUUGUCGCCUAUGGGAAGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCGUUGAAUAGAUUAGCAUGGAAUAAUAAGAUAGGACCUGGGUACUAUUUUGUUGGUUUGCGUACUUAGGUAAUGAUUAACAGGGACAGUUGGGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGAGUUUCUUUAUGUCUCCGUCAGCACCUUAUGAGAAAUCACAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGUUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGCUUGGUUAGUGAAUCUUCACUGGCUGAAGCUUCUUAGAGGGACGUGCAUUCUAUCAGAUGCAGGAAGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGAGAGGCCUGGGCAAUCUUCUGAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAUUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGGCUAGCUCCCUUCAUUGUGGGUUGGCCGCGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq new file mode 100644 index 0000000..ddb3562 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.bracteata.seq @@ -0,0 +1,2 @@ +>d.16.e.A.bracteata +CACCAGGUUGAUUCUGCCUGACACACACGCUCGUCCCAAAGAUUAAGCCAUGCAUGCUUGUGAAGGAAGCGGAACGGCGUACGGCUCAGUAGGACGGACCUAAUCUAUCCAGCACGGGAGGGAUAACCACGGGAAACUGUGGCUAAGACCGGGAUCUGCCGUGCCCUCGGGUGCUGAAGAGCGGCGGUGUGCUGGGCGAGAGUCUGACCUAUUAGCUUGAUGGCGCGGUAAGGGCGGGCCAUGGCGACGAUGGGUGACGGGGAAUCGGGGUUUGAUUCCGGAGAAGGAGGCUGAGAGACGGCUCCUACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCACUCGAGCGGAGGUAGUGACGGGACGUCUAUGGGGAGCUCUUGAUAACUGCGAGGGGCCUCUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGUGUGUGGUGAUUGCUGCAGUUAAAAGGUCCGUAGUCGACGUGUCUGGCGGGGUCUUGAGGUGCGCUCAACGUGCUAGGACCUCCGCGAGUUGCGUUCCGGAGCACUUGGGGGUGAGGGUAUUCCUGCGUGAGAGGUGAAAUUCGGUGAUCGCGGGGGGACCGACGGGGGCGCAGGCGCUCAUCCAGACUGUGUCCUAUGAUCAAGGGCGGAAGCCGUGGUAGCGAAGGUGAUUAGUGACCACUGUAGUCGCGGCCGCAAACGAUGCGUUCCCGCCUGCUGGGCGGAGGGAAACCGAGAGAGCUCUGGGGAUAGUACGAGCGCAAGCCUGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGAGUGGAUCAUGCGGGUUAAUUUGACUCAACGCGGGGCAGCUUACCAGGGCACGCGCGGGUGCGAUCGCGAUGCGAGAUUCUGCGGCGAGUGGUGCAUGGCCGUUUCUAACACGUGGGGUGACCAGUCUGGUUAAGUCCGAUAACGCGUGCCGCCCCGGCCCUGUGCGAAUGGGGGACGACUGCCGACGAGGCAGGGGAAGAGGGGCGAAAACAGGUCCGUAAUGCCCUCCGAAGCCCUGGGCGCCACGCGUGAUACAAUAGCUGCGUCGCGGUUGGGGUCGGGACUGCGGGCUGCGAGGCCAGCACGAACGCGGAAUUCCUAGUAAGCGUGCGUCACCAUUGCGUGCUGAAUGCGUCCCUGUCCUUUGUACACACCGCCCGUCGUUAUUUGAGAUGGUAGUGCGGCCGAGCGGCUGUCCUCGGGCGGCCGCGAGUCCGCCCUGCUAGAUCGAAUACAAGUCGUAACAAGGUAACCANNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq new file mode 100644 index 0000000..3de621e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.capitellata.seq @@ -0,0 +1,2 @@ +>d.16.e.A.capitellata +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGACUAAGCCAUGCAAGUCUAAGUAUAAAUCUUUUACUUUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUCCCUCACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUCAAUACCCUUCUGGGGUAGUAUUUAUUAGAUGGAAACCAACCCCUUCGGGGUGAUGUGGUGAAUCAUAAUAAGCUUGCGGAGYCCGGUGGCGAUGGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGACGGUAAGGUAUUGGCUUACCGUGGCUUUAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCUUGACACAAGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUAUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAACCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUGUGGCGGUUCCUGUGGUCCGAUUUCGGUACUUUCUGGGACUGCCAUCCUUGGGUGGAUCCUGUGUGGCAUUAGGUUGUCGUGCAGGGGAUGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCGUUGAAUAUAUUAGCAUGGAAUAAUGAGAUAGGACCUUGGUACUAUUUUGUUGGUUUGCGCACCGAGGUAAUGAUUAAUAGGGACAGUUGUGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUCUGGAAGACGAACUAAUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGGUUUCGUUACGUCUCCGUCAGCACCUUAUGAGAAAUCACAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGUCCUUUGAGUGAUUUUCACUGAUUCGGGCUUCUUAGAGGGACGUGCAUUCUAUUAGAUGCAGGAAGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUCCUUGGCCGAGAGGCCUGGGCAAUCUUUUGAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGGAUGGUCCGGUGAAGCCUCGGGAUUGUGACCGGUGCCUUUAUUGGUGUCGGUCGCGAGAACUUGUCUAAACCUUAUCAUCUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq new file mode 100644 index 0000000..aee7873 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.castellanii.seq @@ -0,0 +1,2 @@ +>d.16.e.A.castellanii +CGACUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUGUUUAUACGGCGAGACUGCGGAUGGCUCAUUAAAUCAGUUAUAGGUUAUUUGAUGGUCUCUUUUGUCUUUUUUUACCUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCGCAAGGUCCCGAGCGCGGGGGGCGGGGCUUCACGGCCUCGUCCUCGCAUGCGCAGAGGGAUGUAUUUAUUAGGUUAAAAACCAGCAGCCGGCAACGGCUUCAACUCCUGGUGAUUCAUAGUAACUCUUUCGGAUCGCAUUCAUGCCCUCCUUGUGGGGGCGGCGACGAUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUCGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGCGCUCGAUAAGAGUCUUGUAAUUGGAAUGAGUACAAUUUAAACCCCUUAACGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUCUAGGGACGCGCAUUUCAAGCGCCCGUGUCGUCGGGUCAAACCGGCGACUGCGUUGGCGUUGCGGGCUCGGUCCGUCGGUGCCCCACAAAGGGCUACUGGCGUGUCAACCGGCCCGCCCGUCCCCUCCUUCUGGAUUCCCGUUCCUGCUAUUGAGUUAGUGGGGACGUCACAGGGGGCUCAUCGUCGUGCGGCGUCAAAACCGUGGCGGCGGUGGGUCCCUGGGGCCCAGAUCGUUUACCGUGAAAAAAUUAGAGUGUUCAAAGCAGGCAGAUCCAAUUUUCUGCCACCGAAUACAUUAGCAUGGGAUAAUGGAAUAGGACCCUGUCCUCCUAUUUUCAGUUGGUUUUGGCAGCGCGAGGACUAGGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUCUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACCAGCGAUUAGGAGACGUUGAAUACAAAACACCACCAUCGGCGCGGUCGUCCUUGGCGUCGGUCCUUCACGGGGCCGGCGCGAGGGCGGCUUAGCCCGGUGGCACCGGUGAAUGACUCCCCUAGCAGCUUGUGAGAAAUCAUAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAUGCCGCGCUAGCCCGUCCAUCAAAACCCAUGCGUGGCUCACGCGGUCCGCUGCGGGGUGGUGUCACUUCGCGGCGACGUCAUCCCGCCGGCAGGGCCCGGGUCCGUGUGGGCGGUAGGGUUCGGCGUCCGUGCUUCUUAGAGGGACUGCUGCGCGCCUAGCCAGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUUAAUCCAACGAGUCCGCUUCAAUCGAGGCGCGAUGCCGUUGGGGUCAAACCCAACUGCGUCGCUGUCCUCGAUCGCGCCUGGGCCGAUAGGUCCGGGUAAUCUUUGCAAAUUUAAUCGUGCUGGGGAUAGAUCAUUGUAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUCCUCGGAGCCGUGGCCUCUACGCAAUCCGGGCAACCGGGUUGUGAGGUCUCCCCUUUUGGCGGCGAAGUCGAUUGAACCUUACCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUCUCCGUAGGUGAACCUGCGAAAGGAUCAGGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq new file mode 100644 index 0000000..accfe21 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.connecticus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.connecticus +CACCAGGUUGAUUCUGCCUGACGUGGACGCUAGCCUUGAAGAUUAAGCCAUGCAAGCUUGUGAAUAUUAUAUAUGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCCAUAUUAUUUAUAACCACGGGAAACUGUGGCUAAGUAUUAGGAUGAGGAUGUGACCUAUCAGCUUGACGGUACGGUAAGUGCGUACCGUGGCUAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAUUAUUAGUGUAUAUGGUGUGUAUAAACAGCACACCGAAGUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAGUAGCGUCUGUGUUUAUUGCUGCGGUUAAAAUGUGCGUAGUCUGGUUAGUGGUCUGGAGUAAAUCUUUUGUAUCUAACAACAGGGUAUUCUAGAGACUUAUACCUUGAGACAGGGAAGAGGCGAUGAUAUUUGGUAGCGAGAGGUGAAAAUCGAUGACCUACCAAGGAGCACCGGAGGCGAAAGCGAUCGCCGAGAACUGUUCUGACGAUCAAGCGCGUGAGCAGGAGUAUCGAAGAGGAUUAGAGACCCACGUAGUUCCUUGCAGUCAACGAUGCCAACGCUGUGGUGGUAUUUACCAUUGCAGAGGCGAAAGCUAGUGUAUGGGCUCCGGGGAUAGUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCCGGGCAGGCAAUUGUCGAGGGAAGCUAUUGUAGCUGAUGAUAUUGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGAGUGAUCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGAGUGGUUGCUUUUGUGACUAGACGGUGUCUGUAAAGACAAGGAAGCGACACCCAAUAACAGGUCUGUGAUGCCCGUAGAUGUCCGGGGCUCCACGCGCACUACAAUGGGUGGUAGUAUUAGUAAAGUGUAGCUAGCCGUAGUUGGGAUUGACAUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACUAACGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGCGGGUGAAGAUGCGAGCAGUCAGGUGAUGGGGAUAAGUGUUUGUGAGUAAUGAAUGCUUGGAACUGUUGCUGGUAAAUGAUUGUGAGUGUAAGAACCCGUGCAGCUAAAUUGGAUGUAAGUCGUAACAAGGUAACCNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq new file mode 100644 index 0000000..c3ebfab --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.dasyae.seq @@ -0,0 +1,2 @@ +>d.16.e.A.dasyae +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGAGGUAACUCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCUCGUAAGAGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUUCUGACACAGAGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGGGCAGCCCGUGCUGUGCGCGUAGUGCGUGCGGCGCUGGGAUGUUCUUUUGUGGAGGGCGGCGCGUCGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGGGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGAGCCGUUACCAUUGUGUAGCUGUUGCUCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAACGGACCAACGGGUGAGGAUGCGCGAAAGCGUUUCCCAAUCCCUAAAUCCGUUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCCUGGCCGCGGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAAN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq new file mode 100644 index 0000000..4352cb6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.ferocious.seq @@ -0,0 +1,2 @@ +>d.16.e.A.ferocious +CACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUUGAAGAUUAAGCCAUGCAAGCCUGUGAAUACUUGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCACNAACCCUAAUAACCACGGUAAACUGUGGCUAAGGUAGUGGAUGAGGAUGUGACCUAUCAGCUUUGUCGGUACGAUAAGUGCGUACCGUGGCUAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAAGUUAUAUUGAGUGAAUAAAAUACACUCAUAAAUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAAUAGCGUCUGUGUUUAUUGCUGCGGUUAAAACGUGCGUAGUCUGGUUUAUAGCCUGAGUUAAAUACGUGUGCUUUAAGCAUGAAGUAUGUCAGGGACUUAGACCUUGGGAUAGGGACGGGGCAAUGAUAUUCGGCAGCGAGAGGUGAAAAUCGAUGACCUGCUGAGGAGCAACAGAGGCGAAAGCGGUUGUCCAGAACUAGUCCGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGGCGAUUAGAGACCGUCGUAGUUCCUAGCAGUAAACGAUGCCAACACUGUGGUGGAAUGUCACUGCAGAAGCGAAAGCUAGUGUGUAGGCUCCGGGGAUAGUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCUGAGGCAGGCUGUUAGUAGGAGAUUGCUUAGCAAGAUACUGCAGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGGGUGACCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGGAUUCUAUUGUAAAAGGUAGAGACGGUGUAUGUAAGUACAAGGAAGCACCACCCAAUAACAAGUCUGUGAUGCCCGUAGAUGUCCAGGGCUCCACGCGCACUACAGUUUAGUGAAGUGUGUGGAGAGUGAUUUGCUAGGUAGUUGGGAUUGAUGUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACCAACGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGUGGGUNAANUCCAUAGCGAGCUUAGCGAGGUAGUGAUUAUGCACGAGUUAGGUUAGUUAUGGAAAGAACCCAUGCAGCUAGAUUGGAUGUAAGUCGUAACAAGGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq new file mode 100644 index 0000000..b35efec --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.flavus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.flavus +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCACUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUACCUUACUACAUGGAUACCUGUGGUAAUUCUAGAGCUAAUACAUGCUAAAAACCUCGACUUCGGAAGGGGUGUAUUUAUUAGAUAAAAAACCAAUGCCCUUCGGGGCUCCUUGGUGAUUCAUAAUAACUUAACGAAUCGCAUGGCCUUGCGCCGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUACUGAUACGGGGCUCUUUUGGGUCUCGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGUCUGGCUGGCCGGUCCGCCUCACCGCGAGUACUGGUCCGGCUGGACCUUUCCUUCUGGGGAACCUCAUGGCCUUCACUGGCUGUGGGGGGAACCAGGACUUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCCUUUGCUCGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGGACCGCCGUAAUGAUUAAUAGGGAUAGUCGGGGGCGUCAGUAUUCAGCUGUCAGAGGUGAAAUUCUUGGAUUUGCUGAAGACUAACUACUGCGAAAGCAUUCGCCAAGGAUGUUUUCAUUAAUCAGGGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGCGGUGUUUCUAUGAUGACCCGCUCGGCACCUUACGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACAAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAAAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUCUUUUGGAUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUCGGCCCUUAAAUAGCCCGGUCCGCGUUUGCGGGCCGCUGGCUUCUUAGGGGGACUAUCGGCUCAAGCCGAUGGAAGUGCGCGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACAGGGCCAGCGAGUACAUCACCUUGGCCGAGAGGUCCGGGUAAUCUUGUUAAACCCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUGCCUAGUAGGCACGAGUCAUCAGCUCGUGCCGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUCGGUGAGGCCUUCGGACUGGCCCAGGAGGGUUGGCAACGACCCCCCAGGGCCGGAAAGUUGGUCAAACCCGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq new file mode 100644 index 0000000..cd73918 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.fundyense.seq @@ -0,0 +1,2 @@ +>d.16.e.A.fundyense +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUCAAUUUUGUGAAACUGCAAAUGGCUCAUUAAAACAGUCACAAYGCAUUUGGCGAUCAAUUCUAAAUGGAUAUCUGUGGRAAUUCUAUAGUUAAUACAUGCACUAAAACUUAUCUUUGGGGAAAGGUUGUGGUCGUUAGUUACAGAACCAAUUCAAGCUAUGCUUGGACACUUGAAUGAUUCACAAUGACAAAUGAAUUACAUGGCAACAGCUGGUGAUAAUUCAUUCCAGUUUCUGACCUAUCAGCUUUCGACGGUAAGGUAUUGGCUUACCGUGGCAAUGACAGGUGACGGAGGAUUAGGGUUUGAUUCCGGAGAGGGAGCUUGAGAAAUGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGGCACAGGGAGGUAGUGACAAGAAAUAACAAUACAAGGCAUCCAUGUCUUGUACUUGGAAUGAAUGGAUUUUAAACCUUUCUAUAAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCGGUUAAAAAGCUCGUAGUUGGAUUUCUGCUGAGGAUGGCUGGUCCGCCCUCUGGGUGAGUAUUUGGCACAGCCUGAGCAUUUAUCUUGAAAGUACAACUGCACUUGACUGUGUGGUGUGUUAUUGAGAACAUUUACUUUGAGGAAAUCAGAGUGUUUCAAGCAGGUGUUUGGCCUUGAAUACAUUAGCAUGGAAUAAUAAUCAAGAUCGUGGUUCUUUUUUGUUGGUUUCUAGAAUUGAGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUCGUAUUUGAUUGUCAGAGGUGAAAUUCUUGGAUUUGUUAAAGACGGACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUUAAGGGAUCGAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACCAUGCCAACUAGAGAUUGGAGGUUGUUACUUGUAUGACUUUUUCAGCACCCUAUGCGAAAUCAAAGUGUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAAUGAGGAUUGACAGAUUGAUAGCUUUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGUUACAUGUAAUUUCGAUUAUGUGGGCAACUUCUUAGAGGGACKUUGUGUGUAUAAUGCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCUGCACGCGCGCUACACUGAUGUGUUCAACGAGUUUUCAACCUUGCCUGGAAAGGUUUGGUAAUUCUUGAACAGGCAUCGUGAUGGGGAUUGUUUAUUGCAAUUAUUAACCUUCAACGAGGAAUUCCUAGUAAGCUUGAGUCAUCAGCUUGUGCUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGARUGAUCCGGUGAAUAAUUUGGACUGUAGCAAUGUUCAGUUCUUGAACAAUGCAAUGGCAAAUUUAAUGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCUGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq new file mode 100644 index 0000000..1eb2af9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.hermannii.seq @@ -0,0 +1,2 @@ +>d.16.e.A.hermannii +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGGGGCAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGCAAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCAUUUAUAUGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGUGGCCCGUGCUGUGCGCGUAGUGCGUGCGGCGCUGGGGCGCGCUUUUGUGGAGGGCGGCGCGUCGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUACGAUGACCCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGCUACCAUUGUGUAGCUGCUUGUCCCUUCUUAGACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAGAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCUGGCCGCGGUGGAAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq new file mode 100644 index 0000000..52c4664 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.invadans.seq @@ -0,0 +1,2 @@ +>d.16.e.A.invadans +NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACAACUUUGUACUGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUCUACUCGACAGUACCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAUAAAUACCCAACUGCUUGUCGGACGGGUAGCAUUUAUUAGAUUGAAACCAAUUCACUUCGGUGAUUUUGUGUUGAAUCAUAAUAACUGUGCUGAUCGCUCUAAGCGAUAAGUCGAUUGAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGAUAUGGGCCUACCAUGGCGUUAACGGGUAACGGGGAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUUAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCUAAUUUAGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUUUGAGCGUCCGGUCGACGAAAUGUCAGUACUAUGGAUGUUUGGGCCAUAUUUUGUGAGGAUGCCUUUCUGCCAUUGAGUUGGUGGUUGGGUGGACUUGCAUCGUUUACUGUGAAAAAAUUAGAGUGUUUAAAGCAGGCGUUUGCUCAUUUGAAUACAUUAGCAUGGAAUAAUAAGAUACGACCUUGGUGGUCUAUUUUGUUGGUUUGCACGCCAGGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUCAUAUUUCAACGUCAGAGGUGAAAUUCUUGGAUCGUUGAAAGAUGAGCUUAGGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUCAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUGACCAUAAACUAUGCCGACUCGGGAUUGGCAGUCGUUUAAUUAGAAUGACCUUGUCAGCACCGUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCCGCGUGCUAAAUAGUCCUGCUUACCAAUUUGGUAGGUAAGGACUUCUUAGAGGGACUUUCAGUGACUAACUGAAGGAAGUUGGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGGUACGCUCAACGAGUAUAUAACCUUGAUCGAUAGGUCUGGGUAAUCUUUUGAAUACGUAUCGUGCUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAAGUCAUCAGCUUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGACUCGGUGAGAAAUUGGGACCGCUGUUUCGCUUGCUUCAUUGUGAGUGAAACGGUGGGAACUUUUUCUAACCUCGCCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq new file mode 100644 index 0000000..9e4029d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.kariana.seq @@ -0,0 +1,2 @@ +>d.16.e.A.kariana +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAAUCUUUUACUUUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAAUUUAUUUGAUAGUCCCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAUCAAUACUCGACUCACGAAGAGUAGUAUUUAUUAGAUUGAAACCAACCGCUUCGGCGUGAUGUGGUGAUUCAUAAUAACUUUGCGAAUCGCAUGGUUUAACACCGGCGAUGGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGGAAAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUAUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUGUGGUUGGAGAGCUCCUCCGUUCGCUUAGSUUCGUGCUGGAGCUUCUCCGUCCAUCCUUGGGUGGAUCCUGUGUGGCAUUCAGUUGUCGUGCAGGGGAUGCCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUACGCCUUGAAUAUAUUAGCAUGGAAUAAUGAGAUAGGACCUGGGUACUAUUUUGUUGGUUUGCGCACCGAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUCGUAUUCCAUUGUCAGAGGUGAAAUUCUUGGAUUUUUGGAAGACGAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACAAGGGAUUGGCGGUUGUUCGUUUUGACUCCGUCAGCACCUUAUGAGAAAUCACAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCUGCCUGCUAAAUAGUUGGGUGAAUGACUCGUUCAUUGACUACAGCUUCUUAGAGGGACGUUCAUCUCUUAAGAUGAAGGAGGAUAGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUGUUCCUUGGCCGAGAGGCCUGGGGAAUCUUGUUAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGAUCAUCAAUCUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAGCCUCGGGAUUGUGACUGUUCUGCUUUAUUGUGGUCGGUUGCGAGAACUUGUCUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUCUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq new file mode 100644 index 0000000..e28f2e8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.khaliulini.seq @@ -0,0 +1,2 @@ +>d.16.e.A.khaliulini +UCCACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUCGAAGAUUAAGCCAUGCAAGUCUGUGAAUCUUUAUAGAGAAACAGUGAACGGCUCAGUAUAACACGUCUAUCUACCCAUCGUGUGAACAUAACCAUGGUAAACUAUGGCUAAAUUGAUGGAUGAGGAUGUGACCUAUCAGCUUGACGGUACGGUAAGUGCGUACCGAGGCGAUAACGGGUAACGGGGAAUAUGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUAGCAUUUAUAUGUGGUAUGUUUAAAUAGCAUAUCGAAGUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCAAUAGCGUCUGUGUUUAUUGCUGNGGUUAAAACGUGCGUAGUCUGGUUAAUGGCCUGAAGGUAACAUGCAUUUUCAUAGUGUAGGAUAUUUCAGGAACUUAUGCCUUGAGANAGGGAAGGGGUAAUGUUAUUUGGUAGCGAGAGGUGACAAUCGAUGACCUACCAAGGAGCGACAGAGGCGAAAGCGAUUACCAAUAACUGAUCUGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGAGGAUUAGAGACCCACGUAGUUCCUUGCAGUCAACGAUGCCAACGCUGUGGUGAUACUUGUCAUUGCAGAGGCGAAAGCUAGUGUAUGGGCUCCGGGGAUANUACGGACGCAAGUUUGAAACUUGAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCNGGUUAAUUUGACUCAACGCGGGAAAACUUACCCGGGCAGGCAAUUGUCGUGAGAAGCUAUUGUAGCUGAUGAUAUUGCGCGUGGUGCAUGGCCGUUCUUAACACGUGGAGUGAUCUGUCUGGUCAAAUCUGAUAACGCGUGAGAGGUGAGUAUUUGGUUGAGAGACCAAAUAGACGGUGUCUGUAAAGACAAGGAAGCGACACCCAAUAACAGGUCUGUGAUGCCCGUAGAUGUCCGGGGCUCCACGCGCACUACAAUGGAUGGUAGUUUUUAUAAGCGGUAACCAUUCGUAGUUGGGAUUGACAUAUGUAAUUAUGUCAUGAACGUGGAAUUCCUAGUAGUUGGUAGUCACUAACGACUAACGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGAAGUGCGGGUGAAGAUGUGAGUGUAGACCAAUGGGAGGAUCAGUAUACUUGUGUGAGUUGAUUACGCUUGUGUAUUGUGACUGUUGUUAGCAUGAGCAUAAGAACCCGUGCAACUAGAUUGGAUGUAAGUCGUAACAAGGUAANCAUNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq new file mode 100644 index 0000000..cd1bf7e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.macrogynus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.macrogynus +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUAAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGUUUAUACAAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAAUUUAUUUGAUAGUACCCUUUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCACAAAAGUCCUGACCUUUACGGAAGGGAUGCAGUUAUUAGAUACAAAACCAACCCGGGCAACCGGUUUUUUGGUGAUUCAUGAUAACUUUGCGGACCGCAUGGCCCUGCCGGCGGCGGGUCAUUCAAAUUUCUGCCCUAUCAACUGUCGAUGGUAGGAUAGAGGCCUACCAUGGUGAUAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACAAUAAAUAACGAUGCAGGACCUUUUGGUCUUUGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCAAGGGUUUUUUUCGUAGCUAGCCAUUGUUCCCUUUGCGGUCAAUGUGCAUUUGGCUACAGGCCCUUUUUUUCUGCUAGGAGAUGCGGCUCUUCUGCUUGUCAGCGGGGCUGCAGUUUUCCUAGCACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUUUUCUUUGCCUGAAUAUCUUAGCAUGGAAUAAUAGAAUAGGACUUUGGUUCUAUUUUGUUGGUUUCUAGGACUAGAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAGGAAAGACUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAAGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACGAUGCCGACCAGGGAUCGGGCGCUUGUAGUUUUUCCAAAAAGACACGCCCGGCACCUUUUGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUGGUAAGGAUUGACAGAUUGAAAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAUUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUUUCCUACUCGUUACUUGCUCAUGGGUUUUAUCUCAUGGCACGCAAGUUCUUAGCGGGACUGCUGGCGUUUAGCCAGAGGAAGUUCGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGCAGUCAGCAAGUUUUUUAACUGGCUGUAGUUCUUUCGGGAGCUAUGGUCGAUUUCCUUGCCCGAAAGGGUUGGGUAAUCUUUUGAAACUGCAUCGUGAUGGGGAUCGACCUUUGUAAUUAUCGGUCGUGAACGAGGAAUUCCUAGUAAGUGUGGGUCAUCAGCCCACGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGCUUAGUGAGAUUUUUGGAUUGUUGAGCGAUUGCAGCAAUGUGAACGCCCGACGAGAAAUUGAUCAAACUUGGUCAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq new file mode 100644 index 0000000..8d7d7a0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.majus.seq @@ -0,0 +1,2 @@ +>d.16.e.A.majus +NNNNNNNNNNNNNNNNNNNNNNNUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACCUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGACGCAUUUAUUAGAUAAAAGGUCGACACGGGCUCUGCCCGUUGCUGCGAUGAUUCAUGAUAACUUGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACUAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUACGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUCAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACUUUGGGUUGGGCCGGCCGGUCCGCCUCUGGUGUGCACCGGUCGUCUCGUCCCUUCUGCCGGCGAUGCGCUCCUGGCCUYAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUUAUAGGAUUUCGGUCCUAUUACGUUGGCCUUCGGGAUYGGAGUAAUGAUUAACAGGGACAGUYGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGGUAUCCCUCCGCGGCCAGCUUCUUAGAGGGACUACGGCCUUUUAGGCCGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUUAUAGCCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUGUUCGGAUCGCGGCGACGUGGGCGGUUCGCUGCCCGCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUGAGAGGAAGGANNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq new file mode 100644 index 0000000..8870493 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.michaelis.seq @@ -0,0 +1,2 @@ +>d.16.e.A.michaelis +NNNNNGGUUGAUUCUGCCUGACGUAGAACGCUAGUCUCACAGAUUCAGCCAUGCAAGUAGUAUGUAUGUAAUACACAAUGGCUCAGUAUCGAGUAUAGCUUUGCUCUCCAAGAUGUGAUACUUUCAGGAAACAGAAAAUAAAGCAUCUAUCUUCUAAAGUUUUUUAGAGGAGAGGAGAAGAAGCACUCACCUAUCAGUUAGUAGGUAUGGUAAGGGCAUACCUAGACGAAGACGGGUACGGGGAAGGCAACUUCGAUUCCGGAGAGGGCGCCUUUAGAGAUGGCGACCAGUUCUAAGGAGUGCAGCAGGCUCGAAACUUACCGAAUUAUAGAAUAGAGGUAGUGAUGGAAACGUUUAUAUAGAAAUACUGGUAAAGCAAGUAUUAUUAACUGAGGAAAGCUGGUGCCAGCAGCCGCGGUAAUACUUGCUCCAGGAGCUUAUUCGAUAUGUUGCGGUUAAAACGUCCGUAGUCGCGGCUGGGACUGACCUGUAAUCUAUUUGGUCAACAGAUAGAUAGGGGCAGUAGCAAGUUGGAAAAGAGCAAUUUGGUGUCAGCUAAUGGUAUGGGGAGGGGUAAAGUCUGAGGAUCCUGCAGGAGGAGCAAAGGCGUAAGCACUGACAAAGAUUGAUUCUGUUGAUCAAGGACAGAGGCUAGAGGAUCGAAUACGAUUAGAUACCGUAGUAGUUCUAGCAGUGACCGAUGAUGAUUUUGCCUUAUGCAAUAGAGAAAUCAAAAUAGAUCUCCGGGGAGUACAUGCGCACAGGAACUUAAGAAUUGACGGAAGCUAGCCACAAGGGUUGGAUUGUGCGGCUUAAUUUGACUCAAAGCGGAAAAGCUUACCAAGCUUAUUUAUUCAACGAGUAUUUAUCCGAGAGUAAAAUGGUGUGCAUGGCCGUUCCUAACACAUGGAGUGAUUUUGUGAUUAACCUUCCGUAAUCUGUGUAAAUCCUCAUAAUAGCUUGUUUGAAAAGAACAAUUCGAGCAAGAACAGGUCAGUGAUGUCCUUUGAUAGCUUGGGCUGCACGCGCAAUACAAUUUUUAUGUAGUAAGAUAUAGAUAGGGAUUGAGGGCUGAAAGCGCUCAUGAACACGGAAUAGCUAGUAACGUGAGUUCAAUAUACGGCGAUGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUGAUUUUUGAGUCAAUUAUAAUUGGCUACUUGAAUGAGUUAUUCUAAAACCGGUACAAGUCGUAACAAGGCUACGGUUGAAGAAUCAGCAGUAGGAUUAGCG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq new file mode 100644 index 0000000..f9edb71 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.plicata.seq @@ -0,0 +1,2 @@ +>d.16.e.A.plicata +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUCGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGAUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGCAACGCGGGGUAACCCGUGGUACAAGUUAGAUAACAGGCCGACGCUUGACGAUUCAUAACUUUUUUUCUGAUCGCGCCUUGUGCGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGACGUGAAGGUAUUGUCUUCACGUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAAUAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGCUUGCGUAUGUCACCGAUGAUGCGGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGGGCGUCUGGCGGAGAGUAAAUCUUUGUCGGUCGCGCCUGCUUUUGUGGAGGGCGCGAGCGGGCGGCUUUACUGUCGCGCGUUCGCGGCGCCACCGUUUACUGUGAAUAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUUGUCCUUUUUGUUGGUUUGUGAGGCCGAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAGACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGACUGAAUUUGGCCCGCCCGGGACCCUCCGGGAAACCAAAGUGUUUGCUUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGGCGGGCUAUCGCUUGAUAGUACUGACCUUCCUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCCAACCCCCAAACCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUAUCCCUCUUGAACGAGGAAUACCUUGUAGGCGUGGGUCAUCAUCCCGCGCCGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGACUCGGGACCGCGCCGACUAGCGCGUCUAACGCGUUGGUUGUUGUGGAAACUUGUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq new file mode 100644 index 0000000..88f7469 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.scoticae.seq @@ -0,0 +1,2 @@ +>d.16.e.A.scoticae +CACCAGGUUGAUUCUGCCUGACGUGUGUGCUAGUCUUGGGGACUUAGCCAUGCAAGCUAGCGAAGCGGAGCGGAGCGGCGGACGGCUCAGUAGGACGGCGAUAAUUCACCCGCGGCAGAAGAGGGAUAACCGCGGCAAGCUGCGGCUAAGACAAGGGAGGCUGUGUUGCGGGGAGGCGCACGCAGCGGACACGGCGGCGAAGAUGCCGACCUAUCAGCUAGUAGGUAGGGUAAGGGCCUACCUAGGCGACGACGGGUGACGGGGGGUGAGAGCCUGAUACCGGAGAGGGAGCCUGAGAAACAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUGCCCAAUCCCUACGGGGGGAGGCAGCUACAAGACGUGGGGAAGCCCCGGAAAGCACGGCAAAGGAGUGCGUAGCGACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGCACAUGUGUGUUGCUGCAGUUAAAACGUCCGUAGUCGGCCAUGAGGGGCAGUGAGGAAAGGGCUGUGCUCAAGGCGGUGUGCAGCGCGGGACCCGGGGCGAGAGGAACGGACGACGGGCGCGGGAUCUGGGGGCGAGAGGUGAAAAUCGGGGACCCUCUGGGGACGAGCGGAAGCGAAGGCGGCGCCCGAGGACGUGUCCGUUGAUCAAGGACGAAGGCCGGAGGAUCAAAGAUGAUUAGAGACCGUCGUAGUUCCGGCAGUAAACGAUGCCAACGGGGCGAAGCCAAGGGGCUGUGUCCGGGAGAAAUUGGAGUGUUUAGGCUCUGGGGAUAGUACGGUCGCAAGACAGAAACUUAAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAGCUUACCAGUGCCGCAUGCGCGGGAGAUUGGCGGCGGAGCGCCCCCGAGAUUGCGCAGGGAGUGGUGCAUGGCCGUUUGCAACACGUGGGGUGACCUGUCUGGUUGAUUCCGACAACGCGUGAGGCCUAGGGCGCAGGGCUGUGCGACGGGCCGCGGCAAGCGGCAGGAAGGGAGGCGAUAACAGGUCAGUGAUGCCCUCAGAUGCACUGGGCUGCACGCGCACUACAAUGGCGGGGCGAGACGGAGUGCCGAGAGGUGCGAAGGAGGCCUGGCUGCAGCGGGGAUGGGUGCCUGGAAGGGCGCCCUGAACGAGGAAUUCCUAGUAGCCGCGGGUCACCAAGCCGCGGCGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCACUACCUAAGAUGGAUGUGCAGGCGAGGUGGCUGGAGGGAAGGCAGCCGAGCCGGUGCAACUAGAUAAGGUAUAAGUCGUAACAAGGCUACGGUUGANNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq new file mode 100644 index 0000000..54b1917 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.thaliana.seq @@ -0,0 +1,2 @@ +>d.16.e.A.thaliana +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACGAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUAUGGAAGGGACGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGCCCGUUGCUCUGAUGAUUCAUGAUAACUCGACGGAUCGCAUGGCCUCUGUGCUGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUAACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACUGGGCUCUUUCGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGAUGGGUCGGCCGGUCCGCCUUUGGUGUGCAUUGGUCGGCUUGUCCCUUCGGUCGGCGAUACGCUCCUGGUCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGAUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUAUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAAUGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUCACACCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAGUGUUCGGAUCGCGGCGACGUGGGUGGUUCGCCGCCCGCGACGUCGCGAGAAGUCCACUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq new file mode 100644 index 0000000..2598366 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.A.verticilliflorum.seq @@ -0,0 +1,2 @@ +>d.16.e.A.verticilliflorum +NNNNNNNNNGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUAAGAUGGUGAUACUGUGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUUUUUUCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAAUAAAUCUUGACUUUUGGAAGAGGAGCAUUUAUUAGAUAAGAGGUCAAUGCAAGCUUUGCUUGUUGCACUGAUGAUUCAUGAUAAUAGACGGAUCGCAUGGCCCCUGUGUCGGCGAUGCAUCAUUCAAGUUUCUGCCCUAUNAACUUUCGAUGGUAAGAUAUUGGCCUACUAUGGUGUUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUGCGGGGAGGUAGUGACAAAAAAUAACAAUACCGGGCUUUAACGAGUUUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAAUGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUUGGGUUGGGUUUGAUCGGUCUACCUUUGGGUGUGUACCGGUUACCUCGUCCCUCCUACCCAUGAUGCGCUUCUGGCCUUAAUUGGUCGGGUCGUGCCUUGGGUGCUGUUACUUUGAAGAAAUUAGUGUGCUCAAAGCAAGUUUGUGCUCUGGAUACAUUAGCAUGGGAUAACGUCAUAGGAUUUUGAUCCUAUUUGGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGUGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGUCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUACUUUUAGGACUCCGUUGGUACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCGUUAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGUGGAGGUACACCUUCAUGGGUAGCUUCUUAGAGGGACUAUGCCAACUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUUAUAGCCUUGACUAUUAGGUCUGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUUAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUUAUGGCGACGUNNNNGCUUUGCUGUCGGCGAUGUUGUGAGAAGUUCAUUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq new file mode 100644 index 0000000..f2d9e72 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bigemina.seq @@ -0,0 +1,2 @@ +>d.16.e.B.bigemina +UGAAUAGCAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUACAAGCUUUUUACGGUGAAACUGCGAAUGGCUCAUUACAACAGUUAUAGUUUCUUUGGAGUUCGUUUUCCAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACAAGUUCGAGGCCUUUUGGCGGCGUUUAUUAGUUCGUUAACCACUUUUUCUGGUGAUUCAUAAUAAACUUGCGAAUCGCUUUUGCGAUGUUCCAUUCAAGUUUCUGCCCCAUCAGCUUGACGGUAGGGUAUUGGCCUACCGAGGCAGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUUCGUCUUGUAAUUGGAAUGAUGGUGAUGUACAACCUCACCAGAGUACCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUAUUUCAGCCUCGCGUUUUUUCCCUUUUGUUGGGUCUUUUCGCUGGCUUUUUUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGACUUUUGUCUUGAAUACUUCAGCAUGGAAUAAUAGAGUAGGACCUUGGUUCUAUUUUGUUGGUUUUGAGCCUUGGUAAUGGUUAAUAGGAACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACCACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGGGAUUGGAGGUCGUCAUUUUCCGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAGAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGCUGCUUGGAUGUUGUCCUCGUUUGCUUCUUAGAGGGACUCCUGUGCUUCAAGCGUGGGGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUCCAUCGAGUUUGUCCUGUCCCGAAAGGGUUGGGUAAUCUUUAGUGUGCAUCGUGUCGGGGAUUGAUUUUUGCAAUUCUAAAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGGCUUUUCCGAUUCGUCGGUUUUGCCUAGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq new file mode 100644 index 0000000..2c3855a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.bovis.seq @@ -0,0 +1,2 @@ +>d.16.e.B.bovis +NNNNNNNNNNNNNNNNNNNNNNNNNNNNUAGUCAUAUGCUUGUCUUAAAGACUAAGCCAUGCAUGUCUAAGUACCAGCUUGUUACGGUGAGACUGCGAAUGGCUCAUUACAACAGUUAUAGUUUCUUUGGAGUUCACUUUGCUAUGGAUAACCGCGCUAAUUGUGUGGCUAAUACACGUUUGAGGUUAUUACCGCGUUUACUGGUCUUGUGAUUUACAGUAACCUGCGACUCGCUUUUUGCGAUAUUCCAUUCAAGUUUCUGACCCAUCAGCUUGACGGUAGGGUAUUGGCCUCCCGAGGCAUCGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGCGAGACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUACCAAUACGGGGCUACUGCUCUGUAAUUGGCAUGGGGGCGACCUUCACCCUCGCCCGAGUACCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUACUUCACGUCCCCCGCUUGGUCCUUUCCUCGCCGGGACGCCUCGUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGUUUCGCCUGUAUAAUUGAGCAUGGAAUAACCUUGUAUGACCCUGUCGUACCGUUGGUUGACUUUGGGUAAUGGUUAAUAGGAACGGUUGGGGGCAUUCGUACUCGACUGUCAGAGGUGAAAUUCUUAGAUUUGUCGAUGACGCACGACUGCGAAAGCAUUUGCCAAGGACGCUUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCUUAAACUAUGCCGACUAGGGAUUGGUGGUCGUCGCCUCGACUCCGUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAGCGUAAGGAUUGACAGGUUGAUUGUCCUUUCUUGAUUCUCUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAUUUAGUCGCUCGGUCUCCGUCCGUGCGCACUUCAUAGAGGGACUCUGCGGCGUCAAGCUGCGGUGAGGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCUUGCCUCGUGUUUACCCUCGGCCGAUAGGCCUGGUAACCCCUAGUCUGCAUCGUGUUUGGGAUUGAUCUUUGCAAUUCUAGAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGAACCUGCUUGCGCGAUCCGUCGCCGCUCGCGGCCAGGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq new file mode 100644 index 0000000..2699b8a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.canis.seq @@ -0,0 +1,2 @@ +>d.16.e.B.canis +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACAAGCUUUUUACGGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGGUAUUCUUUUUCCAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACACGUUGGAGGCCUUUUGGCCGCGUUUAUUAGUUGUAAACCUCCGCUUGGUUUUCGGUGAUUCAUAAUAAACUUGCGAAUCGCUUUUAGCGAUGGACCAUUCAAGUUUCUGACCCAUCAGCUUGACGGUAGGGUAUUGGCCUACCGAGGCAGCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUAAUGUCUUGUAAUUGGAAUGAUGGUGACUUAAACCCUCACCAGAGUAGCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAACUUGUUGCAGUUAAAAAGCUCGUAGUUGUAUUUUUGCUUGGCGGUUUGUUGCCUUUGUGGCUUGAUUCCGCUUGGCUUUUGGCUUUUUGCCUUAUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGACUUUUGUCUUGAAUACUGUAGCAUGGAAUAAUAGAGUAGGACUUUGGUUCUAUUUUGUUGGUUUGGGAACCUUGGGUAAUGGUUANUAGGAACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGACGUUUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGUGAUUGGAGGUCGUCGUUUGUUUGACCCCUUCAGGAGCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAAACGGUAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGCGCUGGUUACUUGGUUUCCCGCUGCUUCUUAGAGGGACUUUGGGGCUUGAAGCUCCAAGGAAGAUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAUCGAGUGUUGCCCCUGGCCGAGAGGUCUGGGUAAUCUUUAGUAUGCAUCGUGACGGGGAUUGAUUUUUGUAAUUCUAAAUCAUGAACGAGGAAUGCCUAGUAUGCGCAAGUCAUCAGCUUGUGCAGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGGCUAUUCCGAUUCGUCGGUUUUGCCGUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq new file mode 100644 index 0000000..dc4b931 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.coli.seq @@ -0,0 +1,2 @@ +>d.16.e.B.coli +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUAACUACACAGUAAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUACAUUAAAUGGAUAACUGUAGAAAAACUAGAGCUAAUACAUGCCGAGGCCGUAAGGUCGUAUUUAUUAGAUAUUCCAAUUAAGGUGAAUCAUAAUAACUUCGCAAAUCGCGAUUUUGUCGCGAUAAAUCAUCCAAGUUUCUGCCCUAUCAUGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAUCUACGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUGGUGACAAGAUAUAACGACGCAAUUUAUUUUGUGAUUGUAGUGAGGGUAUUCCAAACCGAACCACUAGUACGAUUAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCAAGGCGUGUAUACUCUUUUUGAGUAUGCUACCUACUAGUCUCUGACUGUUACUGUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUUUGCAAGAAUACAUUAGCAUGGAAUAACGAAUGUGUCUAGAAUCUUGGUUAAUUCUAGAUUGCGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUGUUAAAGACUAACGUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGAUAGGGGAUCAAAGACAAUCAGAUACUGUCGUAGUCCUAUCUAUAAACUAUGCCGACUAGGGAUUGGAAUGGUUAUAACGCCGUUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGACUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAACCUGCUAACUAGUCUAAUCCAUUUUAUGGAAUAUGACUUCUUAGAGGGACUAUGUAUUUAAAUACAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAUAUGUCCUGGGCUGCACGCGUGCUACACUGAUGCAUACAACAAGUGCCUAGCCCGCCAGGGUAUGGCAAUCUCGAAUAUGCAUCGUGAUGGGGAUAGAUCUUUGCAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGUGCAAGUCAUCAUCUUGCAUUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUACCGGGUGAUCCGGUGAACCUUUUGGACCGCGAUGCGGAAAAAUAAGUAAACCAUAUCACCUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq new file mode 100644 index 0000000..16f916b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.emersonii.seq @@ -0,0 +1,2 @@ +>d.16.e.B.emersonii +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUAAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUGCUUUAUACAAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAAUUUAUUUGAUAGUACCCCAUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCACUCAAGUCCUGACCGCUUGUCGGAAGGGAUGCAGUUAUUAGAUACAAAACCAGCCCCGGGCAACCGGGUUUUCUGUUGGUGAUUCAUGCUAACUUUGCGGAUCGCAUAGCCUUUGUGCUGGCGACGGGUCAUUCAAAUUUCUGCCCUAUCAACUUUCGACGGUAGGAUAGAGGCCUACCGUGGUGAUAACGGGUAACGGGGAAUAAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUACAGGGAGGUAGUGACAAUAAAUAACGAUGCGGGGCCUUUUGGCCAUCGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAUUUCAGGGCUGUCUUUGUCACCUGGCCACUGAGCCUUURCGGCCAGUGUUGCUUUCGGGUGCGGGCCCUUUAUUUCUGCUGGGUGCUCCUUUGGGUUGGCUUUUGCUAGCUCGGGGGAUGUCUGCCCAGCACGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUUUUUUAAGCUUGAAUAUCUUAGCAUGGAAUAAUAGAAUAGGACUCUGGUUCUAUUUUGUUGGUUUCUGGGACUGGAGUAAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAGGAAAGACUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAAGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACGAUGCCGACCAGGGAUCGGGCGUCAUGUAGUUAUUCACAUAAAAGACGCGCCCGGCACCUUUUGAGAAAUCAAAGUUUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUGGUAAGGAUUGACAGAUUGAAAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAUUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUGAUCUGCUAAUUAGUUGGGCUUGCAUUUAUGCAAGUAAUCCAACUUCUUAGAGAGACUGCUGGCGUUUAGCCAGAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUAAGGUCAGCGAGUUUCAACUUGCUGGCUUAAGUUGAGUUUCGGCUCGGCUUAAGCUGGGAUUCCUUGGCCGUGAGGUCUGGGUAAUCUUUUGAAACCUUAUCGUGAUGGGGAUUGACCUUUGUAAUUAUCGGUCAUGAACGAGGAAUACCUAGUAAGUGUGGGUCAUCAACCCACGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGCUUAGUGAGAUUUUUGGAUUGCCGGGUGAUUGCAGCAAUGCGAACACUUGGCGAGAAAUUGCUCAAACUUGGUCAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq new file mode 100644 index 0000000..3c16027 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gelatinosum.seq @@ -0,0 +1,2 @@ +>d.16.e.B.gelatinosum +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUACGACAAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAAAACGCGGGGUAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGCAAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGUGCGCGCCGGGCUGUGCGCGUAAUGCGUGUGGCGCGGGGCGUGCUUUUGUGGAGGGCGGCCGCUCGUGGCUUAACUGUUGCGGGUGUGCCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGUACCUAUUUUGUUGGUUUGUGAGGGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGUCCGGGACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGUUACCAUUGGUAGCUGUCGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAGAGCGUUUCCCAAUCCCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGACUUGGGACUGCUGCGAUCGGGGUUCAUUCUCUGGCCGCGGUGGGAACUUGUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq new file mode 100644 index 0000000..76f7cfc --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.gibsoni.seq @@ -0,0 +1,2 @@ +>d.16.e.B.gibsoni +NNNNNNNNNNNNNNNNNNNNNNNNNCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUUUUAUAUGGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAAAUUCGUUUCUACAUGGAUAACCGUGCUAAUUGUAGGGCUAAUACAUGAUCGAGGUCCUUCUGGACUGCGUUUAUUAGACUCGAAACCUUCCCGCUUCGGCGGUUCCCGGUGAUUCAUAAUAAACAGCGAAUCGCAUGGCUUUUGCCGGCGAUAAUUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCAGCGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUACGGACACCGUGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUUAAGCUUUGUAAUUGGAAUGAUGGGAAUCCAAACCCCUUCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUCUGCCGCCGGGACUUCGUUCCCUUCGGGCUUCGUUUUCUCGGUGGCAUCCCUCUGGUUAAUUUGGGCCUCGGCCCUCUUUUUCCAGUUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUUUGCCUUGAAUACUUCAGCAUGGAAUAAUAAAGUAGGACUUUGGUUCUAUUUUGUUGGUUUCAGGACCAAAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGCUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACUAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAUUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAACCUCACCAGGUCCAGACAUAGUUAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGCAGCUGAGAAUAAACUUUGUUGUUUCAGCAUUGCUUCUUAGAGGGACUUUGCGGUCAUAAAUCGCAAGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAUCGAGUUUUAUCCUUGCCCGAAAGGGUUAGGUAAUCUUUAGUAUGCAUCGUGAUGGGGAUUGAUUAUUGCAAUUAUUAAUCAUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGUGACGUUUCUAAUUCGUUAGCAACGUCUAGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq new file mode 100644 index 0000000..ee77a35 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.hamifera.seq @@ -0,0 +1,2 @@ +>d.16.e.B.hamifera +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAACUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAAUUUCUUCGAUGGUAAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGGAACGCCGUGGUACAAAUUGGAUAUACAAACCAAUGUUUGGUGAUUCACAAUUUAUUUUCUGAUCGCACUUAUGUGCGACGCAUCGUUCAAAUUUCCGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCCAUCCGGACUCCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGCUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGCGGCGCGGGGCGUCCUCACGGACGGUUCUGCGGCGGCCGCCUUUGUGGAUGGGGGCUAGAGCGAUGUUUCAUUACAUUGCACUAGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAGUAAAUUAGCAUGGAGUAAUAGAAUAGGACCUGUGUUCUGUUUUGUUGGUUUGUGAGGCGCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGGGGCUGUUUUUGGCCCGCCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCGGUUACCGAUUUCUGGUAGCCAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGGGCGAAAGCUUUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGACAGACUGUGUUUCACGGACUGUCUGGCCCGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAAN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq new file mode 100644 index 0000000..f71fd58 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.investiens.seq @@ -0,0 +1,2 @@ +>d.16.e.B.investiens +NNNNNNNNNNNNNNNNNNNNNNNUAUAUGCUUGUCUAAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUCUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCGCAACGCGGGGUAACCCGUGGUACAAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGAACGCAAGUUCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGGGCCCGGUGCUGUGCGCGUAAUGCGUGCGGCGCUUGGGCGCGCUUUUGUGGAGGGCGGCGCGUCGUGGCUUUGCUGUCGCGGUGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUGUCUAUUUUGUUGGUUUGUGAGGGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCAGGCAUUACGAUGACCUGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGUUACCAUUGGUAGCUGCUUGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUUUUAGGAUGCGCGAAAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGAUUUGGGACUGCUGCGAUCGGAGCGUUUACGCUCUGGCCGCGGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq new file mode 100644 index 0000000..d4c4c9b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.macrosporum.seq @@ -0,0 +1,2 @@ +>d.16.e.B.macrosporum +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUCUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGUUAUAGUUUCUUCGAUGUUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAUCACGCGGGGCAACCCGUGGUACGAAUCAGAUAUCAAACCAAUGUAUGGUGAUUCAUGAAUAUUUUUCGGAUCGCACUGUAUGGUGCGACACAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUAUCAUGGUUGUGACAGGUGACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAACUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGCAUAUGCGUCUUCUAAUUGGAAUGAGAACACGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUGUUGGCACGGGCCGGGCUGUGCGCGUCAUGCGUGCGGCCACGGGACGUGCUUUUGUGGAUGGCGGCCGCACGUGGCUUAAUUGUUGCGGGCGUGCCGGCGCCACCAUUUACUGUGAAGAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACGUUAGCAUGGAAUAAUAGAAUAGGACUCGUUUCUAUUUUGUUGGUUUGUCAGUGGCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUCUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACUGCUGCGAAAGCGUUUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGGGCAUUAUGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCGGGUACCCGUGUGGUAGCUGCUGCCCCUUCUUAGACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGGCCAACGGGUGAGGAUACGCGAGAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCUUUGGGACCGCCACGACCGGGGUUUACUCUCUGGCCGCAGUGGAAACUUAUCCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq new file mode 100644 index 0000000..2225903 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mandrillaris.seq @@ -0,0 +1,2 @@ +>d.16.e.B.mandrillaris +NNNNNNNNNNNNNNNNNNNNNNNUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACGGCGAGACUGCGGAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUUCCUUUAUUUUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCCCAAAGUCCCGACUGGGGGUCGCAAGGCUCUCUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCGAUGCAGGGUGGCUUGCUGCCCUGACCCAACGGUGAUUCAUAAUAACUCUAUCGAAUCGCACCAUGGUCCCCUCGUGGGAUCGGCGAUGCUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUCGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUGGCUACCACUUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGUCUUGCAAAAAGACUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUCUCGGAGUGUUUGGCAGGGCUGGUCCGCCGAAAUAGGUGAGCACCGUCCUGCCCGCUCCUCUUGUCCGGGUUCUCAUCCCUGCUAUUCACUUAGUGGGGAACCAAAGGUUCUGUUCCCGCCCUCGGGUGGGGCAGGACUGGAGGCCCGGACCAUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGACAAGUCAAAACUGUCAUUGAAUAUAUUAGCAUGGGAUAAUGGAAUAAGCCUCUCUGCUUAUUUUGUUGGUUUCUAAGUAGGGAGAAAUGAUUGAUAGGGACAGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACCAGCGAUUGGGAGACGUUACACAUGCUGCCCAAAAGGCAGCAUGGAGGACUCCCCCAGCAGCUUGUGAGAAAUCAUAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGUCAUGCCAAUCCUGCUAUUCAAAACCAGGGGGUGAGCGCGGUGCGGUCGGCUCCAAUCUUCGGGUUGGGGUCGGUUCGUGCCCCUUGCCUUCUGGCGGUUGGAUUGGUAGAAGUACUUCUUAGAGGGACAAUCGGUGAUUAGCCGAGGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUUAAUUCAACGAGUGCCACACCUUGGCCGAAAGGUCUGGGUAAUCUUGUGAAAUUUAAUCGUGAUGGGGAUAGAUUAUUGUAAUUGUUAAUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUCUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAAUCUUCGGAGCUCGACCUCUCCGCGAUCCGGGCAACUGGGUCGUGAGGUUGGGCAAAGUCGAUUAAAUCUUACCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq new file mode 100644 index 0000000..5e88cb9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.mediterranea.seq @@ -0,0 +1,2 @@ +>d.16.e.B.mediterranea +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGCUUUAUACUGUGAACCUGCGGAUGGAUCAUUAUAUCAGUUAUAGUUUAUUUGAUAAUCUCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUAAACACCCAACCUCUGGACGGGUGGUAUUUAUUAGAUUGAAACCAAUAUGCUUCGGCAUUUUUGUGGUGAUUCAUAAUAACUUUGCGGAUCGCAUGGCCUUGAGCCGGCGACAGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUGACACGGCGUGGUCGUCUCAAUGAGUCUGUACCGUCGCAUGUGUCGCCAUCCUUGGUUAAAACUUGUCUGGCAUUAGGUUGUCGGGCUUGGGGAUAGCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCCGUUGAAUACAUUAGCAUGGAAUAAUAAGAUAAGACCCAGGUUCUAUUUUGUUGGUUUGCGUACCUAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUUGUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGACAAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUGGCGGUCGUUUUUCCGACUCCGUCAGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGGCGUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUUGGCGUAAUGAAUUUCAUUGCGUACAUCUUCUUAGAGGGACUUUGCGUGACUAACGCAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUAUAACCUUGACCGAGAGGCUGGGUAAUCUUUUAAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGUUCAUCAGACUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAAUUUCGGGACUGACUUUAGGUUGAUUUAUUUCGACUUAAGGUUGGGAACUUACUUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGUGAACCNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq new file mode 100644 index 0000000..341c71c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.1.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.1 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUAUUUUACGCGUGGCGUUUAUUAGACUUUAACCAACCCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAAUUCGCUUCCGAGCGUUUUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUUCCCUUCGGGGUUCUAUUUUCCGGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGUACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq new file mode 100644 index 0000000..e6f2747 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.2.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.2 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCCUUUGGGAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGGCUUGGCAUCAUCUGGAUUUGGUGCCUUCGGGUACUGUUUCCAGGGUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAACCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAGCGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCGAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq new file mode 100644 index 0000000..21c1754 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.3.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.3 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUACGCGUGGCGUUUAUUAGACUUUAACCAGCCCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUUCGAGCGUUAUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUAUCCUUAAUUGGUUACUAUCUUCCAGUAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCCAUUUGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUAUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUAGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACUGAGAAACGUGGAUUCGUCCUUCGUUUUUCGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq new file mode 100644 index 0000000..e92416b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.4.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.4 +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCUUUGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGGCUUGGCAUCUUCUGGAUUUGGUGCCUUCGGGUACUAUUUUCCAGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUCGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq new file mode 100644 index 0000000..ac524f3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.microti.5.seq @@ -0,0 +1,2 @@ +>d.16.e.B.microti.5 +NNNNNNNNNNNNNNNNNNNNNCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUUAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUCGUUUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCUCGAGGCGCGUUUUCGCGUGGCGUUUAUUAGACUUUAACCAACCCUUCGGGUAAUCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUGACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUUAAAGUCUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUUGUCAUUAAUCUCGCUUCCGAGCGUUUUUUUAUUGACUUGGCAUCUUCUGGAUUUGGUGCCUUCGGGUACUAUUUUCCAGGAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAUUCGCCUUGAAUACUACAGCAUGGAAUAAUGAAGUAGGACUUUGGUUCUAUUUUGUUGGUUAUUGAGCCAGAGUAAUGGUUAAUAGGAGCAGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUCUGGGACAAGCUUUGCUGUUCCAGUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUUCCUUGGCCGUCGGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACCAAGAAACGUGGAUUCGUCCUUCGUUUUUUGGAAAGUUUUGUGAACCUUAUCACUUAAAGGAAGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq new file mode 100644 index 0000000..f694c36 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.moritziana.seq @@ -0,0 +1,2 @@ +>d.16.e.B.moritziana +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAAGACUAAGCCCUGCAAGUGCCUGUAUGAGUGUUUAUAUAACGAAACUGCGAAUGGCUCGGUAAAACAGUAAAAAUUUUUUCGGAGAAAAUACUACUCGGAUAACCGUAGUAAAGCUAGAGCUAAUACGUGCUACAAAAUGAGGCGAGCAAUCGUUCUCGUGGUACAAAAUAGAGAUACAACCCAGUUUUUACUGGUGAUUCAUACUUUUUUCUGAUCACACUUUUAUGUGUGUGACGCUCCGAUCAAAUUUCUGACCUAUCAACUAUGAUGGUAAGGUAGUGGCUUACCAUAGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGAACUUCGGGAGGUAGUGACAAGAAAUAGCAAUAGGGGGACCAAUGGUCUCUCUAAUUGGAAUGAAAACAAUGUAAACUCCUUAUUGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAACUUUGGCGAUGGUUGCUGAAACUCCGUAAGGAGAUUGAUGUAGCCUCGUCCUUGUGGAUUUUUGGGGGUGUGGUGGUACUUUAUUGUAUUGCUGCAUUUCCGCCACUGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAAGCGAUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUUCUGUUUUAUUGGUUUGUCUGUAUCAGGUAAUGAUUAACAGGGACGGUCGGGGGCAUUUGUAUUCCAGCGUUAGAGGUGAAAUUCUUGGAUCGUUGGAAGACAAACAGCUGCCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUGUAAACUAUGAGGCCUGGGGAUCGGGCGUGGCCUAUUGGUACGUUCGGCACCCUCCGGGAAACCAAAGCUUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGAAAAUGCUAUUAAACUGCGGUAGCAUCGAAAAUUUAAUCUUCUUAGACGGACUGUAGGCGUAUAGUCUAUGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAAUGGCUCAACGGGUGAGGUAGUGCGAAAGCAUGACCCAAUCUCUAAAUCCAUUCGUGCUGGGGAUAGAAGCUUGCAAUUAUCCUUCUUGAACGAGGAAUACCUUGUAAGCGCGAGUCAUCAUCUCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGAGCUGGGCGAAUUAGUGUUUAUUCACGAAUUUCCUGGUUUAAACUUGGUCAAACCUUACUACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq new file mode 100644 index 0000000..e9dcbc1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.ostreae.seq @@ -0,0 +1,2 @@ +>d.16.e.B.ostreae +NNNNNGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCCAAGUAUAAACACGUUUGUACUGUGAAACUGCAGAUGGCUCAUUAUAACAGUUAUAGUUUAUUUGACAUUGAACUGUUACACGGAUAACCGUAGUAACCUAGGGCUAAUACGUGACAAACCCUGCCUCGGCGGGAGUGCAUAUUAGCUGAAAACCAACUUUGGUUGAAUAAUAAUAUUUGUCGGAUCGCGUUGGCUUCGCCAGCGACAUGUCAUUCAAGUUUCUGACCUAUCAGCUUGACGGUAGGGUAUUGGCCUACCGUGGCUUUGACGGGUAACGGGGAAUGCGGGUUCGAUUCCGGAGAGGCAGCCUGAGAAACGGCUACCACAUCCACGGGAGGCAGCAGGUGCGCAAAUUACCCAAUUCUGACUCAGAGAGGUAGUGACAAGAAAUAACGAUAUGCGGCCAACUGGUUGCUUAUCCGGAAUGAGAACAAUGUAAAAACCUUAUCGAAUUCCAGCGGAGGGCAAGCCUGGUGCCAGCAGCCGCGGUAAUACCAGCUCCGCUAGCGUAUACUAAAGUUGUUGCUGUUAAAACGCUCGUAGUUGGAUAUCUGCCCCCGGGCCGGCCCGGUCGUCCGCGACCGCACACACGUGCAGAGCGGCCGCCCGGGGGCAUAAUUCAGGAACGCCGGUCUGGCCAUUUAAUUGGUCGGGCCGCUGGUCCUGAUCCUUUACUUUGAGAAAAUUAAAGUGCUCAAAGCAGGCUCGCGCCUGAAUGCAUUAGCAUGGAAUAAUAAGACACGACUUCGGCGCCGCCUCGGCGGUUGUUUUGUCGGUUUUGAGCUGGAGUAAUGAUUGAUAGAAACAAUUGGGGGUGCUAGUAUCGCCGGGCCAGAGGUAAAAUUCUUUAAUUCCGGUGAGACUAACUUAUGCGAAAGCAUUCACCAAGCGUGUUUUCUUUAAUCAAGAACUAAAGUUGGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCCAACCAUAAACGAUGUCAACUAAGCAUUGGGCUAUCAAACUUCCUCAGCACUUUUCGAGAAAUCAAAGUUUUCGGACUCAGGGGGAAGUAUGCUCGCAAGAGUGAAACUUAAAGGAAUUGACGGAAGGGCACCACAAGUUGUGGAGCCUGCGGCUUAAUUUGAUUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUAAAGUUCUUUCUUGAUUCUAUGCAUGGUGGUGCAUGGCCGUUCUUAGUCCCUAGGGUGACCCCUCUGGUUAAUUCCGAUAACGGACGAGACCCCACCCAUCUAACUAGCCGGCGCUAACCCGGCGCUCGGCGCCAGUUAGCGGGGUGCAGCAUUGCGCGCCCGGCUUCUUAGAGGGACUAUCUGUGUCUCCAGCAGAUGGAAGAUUGGGGCAAUAACAGGUCAGGAUGCCCUUAGAUGCUCUGGGCUGCACGCGCGCUACAAUGGUGCGUUCAACGAGUUUGACCCGGCUUGACAAGGCCGGGUAAUCUUCAACGCGCACCCAAGUUGGGAUAGAUGAUUGCAAUUGUUCAUCUUGAACAAGGAAUAUCUAGUAAACGCAAGUCAUCAACUUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUUCUACCGAUUGAAUAAUGAGGUGAAUUAGGUGGAUAAGAGCGCUCCGCGUUCUUAGAAGCUUCGUGAACCUUGUUAUUUAGAGGAAGGAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq new file mode 100644 index 0000000..86d81a3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.pacifica.seq @@ -0,0 +1,2 @@ +>d.16.e.B.pacifica +NAACCUGGUUGAUCCUGCCAGUAGUCAUACGCUCGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGCUUUAUACUGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAAUCUCUUACUACAUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUAAACACCCAACUGUUCGCGGACGGGUGGUAUUUAUUAGAUUGAAACCAAUAAGCUUCGGCUUUUUUGUGGUGAUUCAUAAUAACUUUGCGGAUCGCAUGGCCUCGAGCCGGCGACAGAUCAUUCAAGUUUCUGCCCUAUCAGCUUUGGAUGGUAGGGUAUUGGCCUACCAUGGCUUUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAUAAAUAACAAUGCCGGGCCUUUUUAGGUCUGGCAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGUGAGUUCGUUUGGCCGGCCGUAAAGGUCUGUGCCGAAAUGUUAUUCGCCAUCCUUGGUGUAAUCUUGUCCGCCAUUAAGUUGUGUGGGCUUGAGGAUGCCAUCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCCGUUGAAUACAUUAGCAUGGAAUAAUAAGAUAGGACCCUGGUACUAUUUUGUUGGUUUGCGUACCUAGGUAAUGAUUAAUAGGGACAGUUGGGGGUAUUUGUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGACAAACUACUGCGAAAGCAUUUACCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUUAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUGGCGGUCGUUUUUCUGACUCCGCCAGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCCCCGCCUGCUAAAUAGUUGGCGCGAAUGAAUUUCAUUCCGUACAUCUUCUUAGAGGGACUUUGCGUGACUAACGCAAGGAAGUUGGGGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUAUAACCUUGCUCGAGAGGGCUGGGUAAUCUUUUAAACGUGCAUCGUGAUAGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUUCCUAGUAAACGCAGUUCAUCAGACUGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCACCUACCGAUUGAAUGGUCCGGUGAAAUUUCGGGACUGAUCGUUUGGUGGUUCAUUCUGCCUUACGAUCGGGAACUUACUUAAACCUUAUCAUUUAGAGGAAGGUGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAANNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq new file mode 100644 index 0000000..8e89a0b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.plumatellae.seq @@ -0,0 +1,2 @@ +>d.16.e.B.plumatellae +CACCAGGUUGAUUCUGCCUGACGUAUGCGCUUGUCUUGAAGAUUUAGCCAUGCAAGCCAGUGACCGUAAGGAACGGCAGACAGCUCAGUAAUACAGUUAUAAUUUACUCGUAGGAUAUGGAUAACCAUGGAAAACUAUGGCUAAAACAUAGGGAAAAUACCGUCACAGGGAAUUUUGAGGUACUUGAUACGAUUAAGUUUCUGACCUAUUAGCUAGAUGGUAAGGUAAAGGCUUACCAUGGCUGUGAUGGGUAACGGGGGAUUAACGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCUAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUUCCUUAUCGGGAGAGGUAGUGAAGAGACGUGGAAUAUAAUUUAGCGAGGGCAUAUUAAAUGGCAGCCUGUAAACUGGAGGGCAAGCCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAACUAUUGUUGCUGUUAAAACGUCCGUAGUAGAUUAUGCUGUUACUAUGACAAAAAUGUAUAUCUCAAAUGAAAUAUAUAGCAUAGUACAAAGUAAAGAUAGGAACAGAUGAUGGCAGCAGUAUUUAAUAGUUAGAGGUGAAAAUCGAAGACCUAUUAAGGACUAUCAGAAGCGAAAGCGGCUGUCAAGGAUGUCUCCGUUUAUCAAGGACUCAAGCUGGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCCAGCUGUAAACCAUGCCAACUAGGUGAGGCCAUUAGGCUACGCCUUAGGAGAAAUCAAAGUUUUUGGGCUCAGGGGAUAGUACGAAAGCAAUUUUGAAACUUAAAGAGAUUGACGGAAGGAUACCACAAGGAUUGGAUUGUGCGGCUUAAUUUGACUCGACGCGGGACAACUUACCAGGGCCGAAUGUCUAUGAGAUUGGCGAUUUGAGAGAAUUCCCGAGAUUAGACAAAGGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACCUGUCAGGUUAAUUCCGAUAACGCGUGAGGCCCUAAAUGCAACAGUGUUGUAUGACGGACAGUGCAAACUGUAGGAAGGAGGGCGAUAACAGGUCAGUGAUGCCCCCAGAUGUUCUGGGCUGCACGCGCAAUACAAUAUAUGAAAUAGAAUAGAGUGUGAAAACACAUCAUUAAAUUCAUAUGUACCAGGGAUAAGCGCUUGUAAAUGCGUUUUGAACAUGGAAUUCCUAGUAAUCGCAGGUCAUUAUGCUGCGAUGAAUGUGUCCCUGUUCUUCGUACACACCGCCCGUCACUAUCUUAGAUGAAUGUAUAGGUGAAAUGGCUGGACGAAAGAAAGGCAGUUGAACCUGUGCAAUUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGGAGAACCUGUGGCAGGAUCAAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq new file mode 100644 index 0000000..0f910b0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.B.rodhaini.seq @@ -0,0 +1,2 @@ +>d.16.e.B.rodhaini +NNNNNNNNAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGUUUUUAUUACAUGGAUAACCGUGGUAAUUCUAGGGCUAAUACAUGCAUGUGCGUUUACGCAGCGUUUAUUAGACUAAACCAUCCCCUUUGGGUACCGGUGAUUCAUAAUAAAUUAGCGAAUCGCAUGGCUUUGCCGGCGAUGUAUCAUUCAAGUUUCUGACCUAUCAGCUUUGGACGGUAGGGUAUUGGCCUACCGGGGCGACGACGGGUAACGGGGAAUUGGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAACAAUACAGGGCUCAAAGCUUUGUAAUUGGAAUGAUGGGAAUCUAAACCCUUCCCAGAGUAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAGAAGCUCGUAGUUGAAUUUCUGCCUCGUCGUUUAUGCUCGCUUCCAAGCGUUUGUAAUUGACUUGGCAUCUUUGUGGAUUAGUGCGCAAGCAUUUUUCCACUAUUUACUUUGAGAAAACUAGAGUGUUUCAAACAGGCAAUUGCCUUGAAUACUACAGCAUGGAAUAAUAAAGUAGGACUUUGGUUCUAUUUUGUUGGUUUUUGAGCCAUAGUAAUGGUUAAUAGGAGCAGUAGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACCAUAAACUAUGCCGACUAGAGAUUGGAGGUCGUCAGUUUAAACGACUCCUUCAGCACCUUGAGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGUCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCAGGUCCAGACAUAGAAAUGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUUAGGAUAUGGGACUACAUUUCAGUCUCAUUAUCGCUUCUUAGAGGGACUUUGCGUUCAUAAAACGCAAGGAAGUGUAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACACUGAUGCAUUCAACGAGUUUUCCUUGGCCGGAAGGUCCGGGUAAUCUUACAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAGGCGCGAGUCAUCAGCUCGUGCCGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAGUGAUCCGGUGAAUUAUUCGGACUGAAGAACUUAGAUUCGUCUAAAGUUUUUUGGGAAGUUUUGUGAACCUUAUCACUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCNNNN diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq new file mode 100644 index 0000000..32b6e40 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.albicans.seq @@ -0,0 +1,2 @@ +>d.16.e.C.albicans +UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUACCUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCCCGACUGUUUGGAAGGGAUGUAUUUAUUAGAUAAAAAAUCAAUGCCUUCGGGCUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAAAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGCUUGGCUGGCCGGUCCAUCUUUUUGAUGCGUACUGGACCCAGCCGAGCCUUUCCUUCUGGGUAGCCAUUUAUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCUUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUAUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGUAUCAGUAUUCAGUUGUCAGAGGUGAAAUUCUUGGAUUUACUGAAGACUAACUACUGCGAAAGCAUUUACCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGUUGUUGUUCUUUUAUUGACGCAAUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGCUGCUAGCAUUUGCUGGUAUAGUCACUUCUUAGAGGGACUAUCGACUUCAAGUCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUAUAAGCCUUGGCCGAGAGGUCUGGGAAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUGUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGGCCUCCGGAUUGGUUUAGGAAAGGGGGCAACCUCAUUCUGGAACCGAGAAGCUGGUCAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq new file mode 100644 index 0000000..69158d5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.citrina.seq @@ -0,0 +1,2 @@ +>d.16.e.C.citrina +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCCCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGCGUCGAAGUGAGCUCGUUGCUUGUACUGAGAUGCCCUUCCAUCCUACUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGUUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGACCCGUUGCUUAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGUGGCCUUUAGGCUGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq new file mode 100644 index 0000000..b680862 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.crispus.seq @@ -0,0 +1,2 @@ +>d.16.e.C.crispus +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAACUACUACUUGGAUACCCGUAGUAAUUCUAGAGCUAAUACAAGCCUUAAAGCGACAUUUAUGUCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACAAUUUCUUUUCUGAUCGCACGUUAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGAGUGACGGAUCGUGGGUGCGAGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGAUACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAACGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAGGUUGGCGGGCAGUCCAGGGCGUCCUCGCGGACGGAUCUGGAGUUGGCCGCCUUUGUGGAUGGGGGCCUAGUGGAGCUUCACUGCUUCAUUGUGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUCCUGUUUUGUUGGUUUGUGAGGAUCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGGCGGAAGACAAACGGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGGAGGACUGUAUUUUGGCCUACCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCAGUACCGUUUUUUGGUACUGAGGCUUGCCUUCCUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAACUUUCCCUCUUGAACGAGGAACACCUUGUAAGCGUGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGAUGGAUGGAUUGUGUUUCACAAACUAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGACAGAAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq new file mode 100644 index 0000000..275fcb0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.lunata.seq @@ -0,0 +1,2 @@ +>d.16.e.C.lunata +CACCAGGUUGAUUCUGCCUGACGUGGACACUUGCCUUGAAGAGUAAGCCAUGCAAGCUUGUGAAUAAAUCCUGAAACAGUGAACGGCUCAGUAGAACACAUUUCAUCUACCCAAGUUAAAAAUAACCAUGGGAAACUAUGGCUAAAUAUAAUUUGGAUGAGAGUGUGACCUAUCAGCUAGUAGGUACGGUAAGAGCGUACCUAGGCUAUGACGGGUAACGGGGAAUCAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUGAACAUUGAGGUAGUUACGAGGCGUACCUAUGUAAUAUAAUUAUAUAGGGAUGAGGUAUGAUUUCAAAUCAUGCACGACAUACUGGAGGGCAAGGCUGGUGCCAGCAGCUGCGGUAAUUCCAGCUCCAGUAGUGUCUAUGUAAAUUGUUGCGGUUAAAACGUGCGUAGUCUGAUUUGCGAGAUCUAAAGUAAAGAUGCUUUUAUCUAAAAGUAGAAUAUUUUAGAGAUCAAAAAUCUUGAGACAGAGGAGAGGUAACGAAAUUCGAUGGCGAGAGGUGAAAAUUGAUGACCCAUCGAGGAGAAACAGAGGCGAAAGCGGUUACCAGAAGCUGUUCUGACGAUCAAGCACGUGAGCAGGAGUAUCGAAGGCGAUUAGACACCGUCGUAGUUCCUUGCAGUAAACGAUGCCCACACUGAUGUGCUUAACGCAUGUCAGACGCAAAAGUUAAAGUGAGGCUCCGGGGAUAGUACGGUCGCAAGAUUGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGAAAACUUACCAGUACAGAUUACUAUCGUAUGAAGGAAUACCUGAUGAUGUAAUACGUGGUGCAUGGCCGUUCUUAACACGUGAAGUGAUUCCUCGUGUCAAAUCAGCUAACGCGUGAGAGGCGAGUCUUAUUUUAUAAAUAAGAGACGGCAUAGGCAACUAUGAGGAAGCAACGCCCAAUAACAGGUCCGUGAUGCCCGUAGAUGUUCUGGGCUCCACGCGCACUACAAUUAUAAAUACUAUUUUGUAAUUUAUAAUCAGUAGGGAUUGUUUGUUGUAAAACUUACAUGAACGUGGAAUUCCUAGUAUAUAGAUGUAAGCAACGUCUAUUGAAUAUUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGUUAUUAGGGGGAAGCUGAUAUAUUAUAUCAGAAGACUUCUGGUAACUAGAUUGGAUGUAAGUCGUAACAUGGUUGCAGUAGGUGAACCUGCCGCAGAUCAGUAG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq new file mode 100644 index 0000000..0bf8af5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.neoformans.seq @@ -0,0 +1,2 @@ +>d.16.e.C.neoformans +UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACGAAUUCAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUAUCUUGCUACAUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUGAAAAGCCCCGACUUCUGGAAGGGGUGUAUUUAUUAGAUAAAAAACCAAUGGGUUUCGGCCCUCUAUGGUGAAUCAUAAUAACUUCUCGAAUCGCAUGGCCUUGUGCCGGCGAUGCUUCAUUCAAAUAUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUAUCAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGGCUCUUUUGGGCCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUCGAACUUCAGGUCUGGCGAGGCGGUCCUCCUCACGGAGUGCACUGUCUUGCUGGACCUUACCUCCUGGUGGUCCUGUAUGCUCUUUACUGGGUGUGCAGGGGAACCAGGAAUUUUACCUUGAAAAAAUUAGAGUGUUCAAAGCAGGCAAUCGCCCGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGGAUCGCCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUUGGUAUUCCGUUGCUAGAGGUGAAAUUCUUAGAUUGACGGAAGACCAACAACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAGGUUAGGGGAUCAAAAACGAUUAGAUACCGUUGUAGUCUUAACAGUAAACGAUGCCGACUAGGGAUCGGCCCACGUCAAUCUCUGACUGGGUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAACCUGCUAAAUAGUCAGGCCGGCUUUGGCUGGUCGUUUGACUUCUUAGAGGGACUGUCGGCGUCUAGUCGACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACUGAGCCAGCGAGUCUUACCGCCUUGGCCGAGAGGCCUGGGUAAUCUUGUGAAACUCAGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUACCUAGUAAGCGUGAGUCACCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGAUCUCCGGAUUGGCGUUGGGGAGCCGGCAACGGCACCCCUUGGCUGAGAAGCUGAUCAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAGUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq new file mode 100644 index 0000000..6c217f5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.officinalis.seq @@ -0,0 +1,2 @@ +>d.16.e.C.officinalis +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAAGACUAAGCCAUGCAAGUCUAAGUAUGAGGAAUAAUUAAGACGAAACUGCGAAUGGCUCGGUAAAACAGCAAUAAUUUCUUCGGUGAUUUUUACUACUCGGAUAAUCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAUGCUUGGGUUUACUCAGGCAGUGCCGUUUAGAUAACAACACCAACAUAUGGUGAUUCAUAAUCGUCUUUCGGAUCGCUGGCGAAAGCCGGCGACGCACCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAGUGUCUUACCAUGGUGGCAACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCAGACUCUGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGACCCAUAAAGUCUUCUAAUUGGAAUGAGAACAAGCUAAACAGCUUAUCGAGAAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGACUUUGGCAAUUCCGGAUGUGUGCGCGUCGUGCGCGCACUUUGCAGGGGUUGCUUUUGUGGGCAUGCGUGGGAUGAUGCGACUUUAUUGUCGAACGUCCCUACGCAACCACCUUUUACUGUGAGAAAAUUAGAGUGUUCAAAGCAGGCAAUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGGUCUUAUUUUGUUGGUUUGUUAGGGCUGAGUAAUGAUUAAGAGGGACAGUUGGGGGCAUUUGUAUUCAGGCGCUAGAGGUGAAAUUCUUAGAUUGCUGGAAGACAAACUGCUGCGAAAGCGUCUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGAGGAAUAUCGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGGGCUACUACCAUUUUGGUAGUACGUUUUCCCCUUCUUAGACGGACUGUGGGCGUCUAGUCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGUGGAUCAGCGGGUCAGGUUGCACGAAAGUGUUUCCUAAUCUUUAAAUCCGCUCGUGAUGGGGAUUGACGGUUGCAAUUUUCCGUCAUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCUUUGGGAUUGCGAUGGAAAGAGCGUCUCGCUCGUUCUGUCGUGAGAACUCAGUCGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq new file mode 100644 index 0000000..bb1658f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.paradoxa.seq @@ -0,0 +1,2 @@ +>d.16.e.C.paradoxa +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACUAUUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGGUACCUUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCAACAAAUCCCGACUUCUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCAACACCGGGCAACCGGAUCCCUUGGUGAUUCAUAAUAACUUCUCGAAUCGCAUGGCUUUACGCCGGCGAUGCUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUAGUAACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGCGCCUGAGAGAUGGCGACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCGCAACUCGCGGAGGUAGUGACAAUAAAUAACAAUACGGGGCUUUUCAAGUCUCGUAAUUGGAAUGAGAACAAUUUAAAUCCCUUAUCGAGGAUCCAUUGGAGGGAAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUCGGAUUUCGGGGCGGGGCAGUCGGUCUGCCUAAUAGGUGUGUACUGGCUGUACCCGUCCUUCCUUCCGGGGAUGGGUGCUGCUCUUAACUGAGUGGCAUUCAGACACGGAUCUUUUACUUUGAGUAAAUUGGAGUGUUUAAAGCAGGCCUACGCUCUGAACAUUAUUAGCAUGGAAUAAUAAAAUAGGACCCUGGUUCUAUUUUGUUGGUUUCUAGGAUUGGGGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUCAUAUUCCGUUGUCAGAGGUGAAAUUCUUGGAUUUACGGAAGAUGAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACGAUGCCGACUUACGAUCAGCAGGUGUUAAUUUAACGACCCUGUUGGCAGUAUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUACUAAAUAGUUACACGAACUUCUAGUUCGUGGUCAACUUCUUAGAGGGACUAUUUGUGUCUAAUGAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACGAAUUCAACGAGUUUUUCCUUGACCGAUAGGUCUGGGUAAUCUUUGAAACUUCGUCGUGAUGGGGAUAGAUCAUUGCAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUCGGUCCGGUGAAAUCUUCGGAUCGUGGCCAUGUACCUGGUCUCCAGGAACAAGGUCGCGAGAAGUUGAUUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq new file mode 100644 index 0000000..2b1cbde --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.C.rubrum.seq @@ -0,0 +1,2 @@ +>d.16.e.C.rubrum +CACCCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAAUACGUGCCAUACGGCGAGGUUUUACCUCGUGGUACUAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACACUUAUUUUUCUGAUUGCACAUUUUUUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUUUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCAAUGGGUUUUCUAAUUGGAAUGAGAACACGGUAAACAUCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGACGUUGGCGGGCGCCUCGAGUCGGCCUCACGGUCGAUCUUGUUGGCGGCCGCCUUUGUGGAGGGGGGCUUAGGUCGGUGCUUUAUUGUCACUCCUUUGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUCCUGUUUUGUUGGUUUGUGAGUAUCAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACCAUAAACUAUGAGGACUGGGGAUCGGGCGUGGCUAUUUGGUACGCUCGGCACCCUUCGGGAAACCAAAGUAUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCAGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACUUGGGCGUGCUAGCUAGGCGCUGUUACCAUUUCCGGUAGCGAGGCGGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAAAGCAUUUCCCAAUCUCUAAAUCCGCUCGUGAUGGGGAUAGAGGCUUGCAACUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGUCUGCAUGUCCUGUGUUUCACUUGUGUGCAGGUUGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq new file mode 100644 index 0000000..658da2a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.D.melanogaster.seq @@ -0,0 +1,2 @@ +>d.16.e.D.melanogaster +AUUCUGGUUGAUCCUGCCAGUAGUUAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACACACGAAUUAAAAGUGAAACCGCAAAAGGCUCAUUAUAUCAGUUAUGGUUCCUUAGAUCGUUAACAGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCAAUUAAAACAUGAACCUUAUGGGACGUGUGCUUUUAUUAGGCUAAAACCAAGCGAUCGCAAGAUCGUUAUAUUGGUUGAACUCUAGAUAACAUGCAGAUCGUAUGGUCUUGUACCGACGACAGAUCUUUCAAAUGUCUGCCCUAUCAACUUUUGAUGGUAGUAUCUAGGACUACCAUGGUUGCAACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCACUCCCAGCUCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCAUAUCCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACAAGGACCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCGGUUAAAACGUUCGUAGUUGAACUUGUGCUUCAUACGGGUAGUACAACUUACAAUUGUGGUUAGUACUAUACCUUUAUGUAUGUAAGCGUAUUACCGGUGGAGUUCUUAUAUGUGAUUAAAUACUUGUAUUUUUUCAUAUGUUCCUCCUAUUUAAAAACCUGCAUUAGUGCUCUUAAACGAGUGUUAUUGUGGGCCGGUACUAUUACUUUGAACAAAUUAGAGUGCUUAAAGCAGGCUUCAAAUGCCUGAAUAUUCUGUGCAUGGGAUAAUGAAAUAAGACCUCUGUUCUGCUUUCAUUGGUUUUCAGAUCAAGAGGUAAUGAUUAAUAGAAGCAGUUUGGGGGCAUUAGUAUUACGACGCGAGAGGUGAAAUUCUUGGACCGUCGUAAGACUAACUUAAGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGAGGUUCGAAGGCGAUCAGAUACCGCCCUAGUUCUAACCAUAAACGAUGCCAGCUAGCAAUUGGGUGUAGCUACUUUUAUGGCUCUCUCAGUCGCUUCCGGGAAACCAAAGCUUUUUGGGCUCCGGGGGAAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCGAACAUAAGUGUGUAAGACAGAUUGAUAGCUCUUUCUCGAAUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCAAAUAUAUUAAAUAGAUAUCUUCAGGAUUAUGGUGCUGAAGCUUAUGUAGCCUUCAUUCAUGUUGGCAGUAAAAUGCUUAUUGUGUUUGAAUGUGUUUAUGUAAGUGGAGCCGUACCUGUUGGUUUGUCCCAUUAUAAGGACACUAGCUUCUUAAAUGGACAAAUUGCGUCUAGCAAUAAUGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCUGCACGCGCGCUACAAUGAAAGUAUCAACGUGUAUUUCCUAGACCGAGAGGUCCGGGUAAACCGCUGAACCACUUUCAUGCUUGGGAUUGUGAACUGAAACUGUUCACGAUGAACUUGGAAUUCCCAGUAAGUGUGAGUCAUUAACUCGCAUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUUAUUUAGUGAGGUCUCCGGACGUGAUCACUGUGACGCCUUGCGUGUUACGGUUGUUUCGCAAAAGUUGACCGAACUUGAUUAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq new file mode 100644 index 0000000..dcf55c6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.aediculatus.seq @@ -0,0 +1,2 @@ +>d.16.e.E.aediculatus +AAUCUGGUUGAUCCUGCCAGUAGUCAUACGCUUGUCUCAAGGAUUAAGCCAUGCAUGUCUAAGUAUAAAGGAUUUAUAAUGAAACUGCAAAUGGCUCAUUCAAACAGUUAUAGUUUAUUUGAUAUUCAAGCUAAUAUUCUUAUUAGUUAAAUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGUUACGGGGAACUUUACGGGACCCCAGCGUUUAUUAGAUUUAAACCAAUAUUCCGCAAGGUCUACUGAGAUGAUUCAUGAUAACUGAUCGAAUUGCUGGAACUCUAGCAAUAAAUCAUGUAGGUUUCUGCUUCCCAUCAGCUUGAUGGUAGUGUAUUGGACAACCAUGGCAUUCACGGGCUAUCGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAUAAACGGCUACCACUUCUACGGAAGGCAGCAGGCGCGAAAAUUAUCCAAUCCUGAUUCAGGGAGGUAGUGAAAGAAAUAAUGAACUAGGAUUUAUCCUGGGAUCACAAUGGGCUUGAUUUGCAAACACUUAGCGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGAGUAUAUAAACGUUCCUGCAGUUAUUCGAUGCUCGUAGUUGGAUUUCUGAGGUUGAGACGGGAGGGUGGCUAUGGCCAUCGCCCGACUCUUUCCUCAUCCACCUGUUUGCGAAGUCCGGGAUUGAUUUCUCGGCUUCGGGCGCAGUAUCUUACCAUUUCAAUAUUCGUAGUCUUCAUCGAUUAUGUUGUUUCUUUGAGCAAAUUAUAGUGUUUCAGGCAGGCGUGCGCCGGAAUACAUUAGCAUGGUAUAAACGAAUUGGACCGUGUGCCCGUAACUGGGCUUCUCCUUAUUGUUGGUUUGAAGGACACGGAGAUGGUUAAUAGGGACAGCGUUUAUUUCACAAGGAGGCAUUAGUAUUUAAUUUCCAGAGGUGAAAUUCUUUGAAAUAUUAAAGACUAACUUAUGCGAAAGCAUCGUUUGCCAAUGAUGUUUUCAUUAAUCAUUGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACGUUGCCGACUAGGGAUCGGAGGGCGUGCACAAUCCGCCUUCGGCACCUUACGAGAAAUCAAAGUCUUUUGGGUUCUGUGGGUAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAUCUUACCAGGUCCAGACAUAGCGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUAUUUUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUCGUCUGGUUAAUUCCGUUAAACGAACGAGACCUCAGCCUGCUAAAUAGUUGCUCGCCUUUUCUAUAAGACUUGACAACUUCUUAGAGGGACUUUGUGUGCAACCACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUACGUACAACGAGGUAUAUGUACUUGUACAUCAAUGCUGCUCCGAAAUAGACGAGCUUAAUCUUAUAAAUACGUAUCGUGCUGCGGAUAGAUCGUUGAAAUUAUGAAUCUUGAAGGUGGAAUUCCUAGUAAGCGCACGUCACUAACGUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCAAUUUCGAGUGAUCUGGUGAACCUCUUUGGACUGUCGAGCAAUCGCGAAAUUAGAGUGAACCUGACUACUUAGCAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAAUCUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq new file mode 100644 index 0000000..2b84de0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.bieneusi.seq @@ -0,0 +1,2 @@ +>d.16.e.E.bieneusi +CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGUCUCUGAGAUUAAGCCAUGCAUGUCAGUGAAGCCUUACGGUGGAACGGCGAACGGCUCAGUAAUGUUGCGGUAAUUUGGUCUCUGUGUGUAAACUAACCACGGUAACCUGUGGCUAAAAGCGGAGAAUAAGGCGCAACCCUAUCAGCUUGUUGGUAGUGUAAAGGACUACCAAGGCCAUGACGGGUAACGGGAAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUGUCCACUCCUUACGGGGGAGACAGUCAUGAGACGUGAGUAUAAGACCUGAGUGUAAAGACCUUAGGGUGAAGCAAUUGGAGGGCAAGCUUUGGUGCCAGCAGCCGCGGUAACUCCAACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAGGGUCCGUAGUCGUGAAUGCAAUUAAAUGUCGUUGUUCAAUAGCGAUGAGUUUGCUAAUGUUUGCGGAACGGAUAGGGAGUGUAGUAUAGACUGGCGAAGAAUGAAAUCUCAAGACCCAGUUUGGACUAACGGAGGCGAAGGCGACACUCUUAGACGUAUCUUAGGAUCAAGGACGAAGGCAGGAGUAUCGAAAGUGAUUAGACACCGCUGUAGUUCCUGCAGUAAACUAUGCCGACAGCCUGUGUGUGAGAAUACGUGGGCGGGAGAAAUCUUAGUGUUCGGGCUCUGGGGAUAGUACGCUCGCAAGGGUGAAACUUAAAGCGAAAUUGACGGAAGGACACUACCAGGAGUGGAUUGUGCUGCUUAAUUUAACUCAACGCGGGAAAACUUACCAGGGUCAAGUCAUUCGUUGAUSGAAUACGUGAGAAUGGCAGGAGUGGUGCAUGGCCGUUGGAAAUUGAUGGGGCGACCUUUAGCUUAAAUGCUUAAACCAGUGAGACCUCCUUGACAGGUGUUCUGUAACACAGGAGGGUGGAGGCUAUAACAGGUCCGUGAUGCCCUUAGAUAUCCUGGGCAGCAAGCGCAAUACAAUAUCUCUUCAGUAGACAAAGUGAUUUGAGAUGAGUAGGAUCUACGUUUGUAAAUACGUAGUGAAUAAGGAAUUCCUAGUAACGGUGCCUCAUCAAGGCAUGGUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUUUCAGAUGGUCAUAGGGAUGAAGAGCUUCGGCUCUGAAUAUCUAUGGCUAGAUAAAGUACAAGUCGUAACAAGGUUUCAGUUGGAGAACCAGCUGAAGGAUCAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq new file mode 100644 index 0000000..74a3bfa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.cuniculi.seq @@ -0,0 +1,2 @@ +>d.16.e.E.cuniculi +CACCAGGUUGAUUCUGCCUGACGGAUGCUAUUCUCUGGGGCUAAGCCAUGCAUGCUUGUGAACUCUUUGUGGGGGAUUAGCGGACGGCUCAGUGAUAGCACGAUGAUUUGUUUGCGGGAUGAGCAGUAGCUGCGGGAAACUGCAGAUAGUGGUCUGCCCCUGUGGGGUUGGCAAGUAAGUUGUGGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGCAGACGGGAUACGGGGGAUCAGGGUUUGGUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUUGGGGAGGCGGUUAUGAGAAGUGAUGUGUGUGCGAGUGCAAAGGGGUCGCAUGUGAUUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCAAUAGUGUCUAUGGUGGAUGCUGCAGUUAAAAUGUCCGUAGUCUGUUGUGUAUGUCUUUGUGUGUGAUGUUUGUGGUUGUGUGUGGAUGUAGUGAUGUGUGUGGCAGAGGACGAGGGGCACUGGAUAGUUGGGCGAGAGGUGAAAUGCGAAGACCCUGACUGGACGAGCGGAAGCGAAGGCUGUGCUCUUGGACUAAUGUUGCGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACAGUGUGUGUUGUCCAUGAGAAAUCUUGAGUAUGCGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGCUCUGAAGGAUGCCUGUGAGUGCAUGGCAUGAGGCAUGCGGCGGUGGUGCAUGGCCGUUUUAAAUGGAUGGCGUGAGCUUUGUCUUAAGUUGCGUAAGAUGUGAGACCCUUUGACGGUGUUCUACGGAGCAAGGAGGGGAUGGAAAAGAACAGGUCCGUUAUGCCCUGAGAUGAGGCGGGCUGCACGCGCAUACGAUAGAUGGCGCUUCUGCCUGCUGUGAGGGAUGAAGCUGUGUAAGGGGCUUCUGAACGUGGAAUUCCUAGUAAUAGCGGCUGACGAAGCUGCUUUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGACGCACUGGACGAAGAUCGGAAGGUCUGAGUCCUGAGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq new file mode 100644 index 0000000..f6afe21 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.hellem.seq @@ -0,0 +1,2 @@ +>d.16.e.E.hellem +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAUUCUCUGGGGCUAAGCCAUGCAUGUUUAUGAAGCCUUUAUGGGGGAUUGACGGACGGCUCAGUGAUAGUACGAUGAUUUGAUUGGGUGCCUGGAUGUAACUGUGGGAAACUGCAGGUAAGUUCUGGGUGUGGUAGUUUUUAGCUACUGCGUACCGAGUAAGUUGUAGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGGAGACGGGAGACGGGGGAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUAUUGGGGAGGCGGUUAUGAGAAGUAAGAUGUUUAGCAAGUAUAAAUUUGUUGUGAUUUACUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCAGUAGUGUCUAUGGUGAAUGCUGCAGUUAAAAUGUCCGUAGUUGUUUGUAUGUCUUUUGUGUGAUGUUUAUAGUUUUUAGUGGAUGUAGUUUGGUUGUAGCAGAGGACGAGGGGCACUGGAUAGUUGGGCGAGGGGUGAAAUACGAAGACCCUGACUGGACGAAGAGAAGCGAAGGCUGUGUUCUUGGACUUUUGUGGUGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACUGUUUUAGUGUUGUCCGAGAGAAAUCUUAAGUAUGUGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGUUCUGAAGUGAGUGUGAGAGUGUUUUUACAUGAUGCUUACGGCGGUGGUGCAUGGCCGUUUUAAAUGGAUGGCGUGGGCUUUGGAUUAAGUUACGUAAGAUGUGAGACCCUUUUUGACUGUGCUCUAUGGGGCAAGGAAGGAAUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGAAGCGGGCGGCACGCGCACUACGAUAGAUGCCUAUGUGGGCUACUGUGAGGGAUGAAGCUGUGUAAUGGGCUUCUGAACGUGGAAUUCCUAGUAAGAAUGAUUGAACAAGUUAUUUUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGACGCAGUGGACGAAGAUUGAGAGGUCUGAGUCUUUCGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq new file mode 100644 index 0000000..ad17f45 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.histolytica.seq @@ -0,0 +1,2 @@ +>d.16.e.E.histolytica +UAUCUGGUUGAUCCUGCCAGUAUUAUAUGCUGAUGUUAAAGAUUAAGCCAUGCAUGUGUAAGUAUAAAGACCAAGUAGGAUGAAACUGCGGACGGCUCAUUAUAACAGUAAUAGUUUCUUUGGUUAGUAAAAUACAAGGAUAGCUUUGUGAAUGAUAAAGAUAAUACUUGAGACGAUCCAGUUUGUAUUAGUACAAAAUGGCCAAUUCAUUCAAUGAAUUGAGAAAUGACAUUCUAAGUGAGUUAGGAUGCCACGACAAUUGUAGAACACACAGUGUUUAACAAGUAACCAAUGAGAAUUUCUGAUCUAUCAAUCAGUUGGUAGUAUCGAGGACUACCAAGAUUAUAACGGAUAACGAGGAAUUGGGGUUCGACAUCGGAGAGGGAGCUUUACAGAUGGCUACCACUUCUAAGGAAGGCAGCAGGCSCGUAAAUUACCCACUUUCGAAUUGAAGAGGUAGUGACGACACAUAACUCUAGAGUUGAGUAAAAUCAAUUCUUGAAGGAAUGAGUAGGAGGUAAAUUCUCCUACGAAAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGUGUAUAUUAAAGUUGCUGUGAUUAAAACGCUCGUAGUUGAAUUAAAAUGUGGUUUUAUACAUUUUGAAGACUUUAUGUAAGUAAAGUUUCUAGAAAUGUUAAAUUAAAAUCAAAGAAGGAAACAAUUCAAGUAAUUGAGUUGUUAUUACUUUGAAUAAAAUAAGGUGUUUAAAGCAAAACAUUAUGUUAAUGAAUAUUCAAGCAUGGGACAAUGCUGAGGGGAUGUCAAUAAGACAUUUCGAGAGAAGGAUUAAAAGGAACAAUUGGGGUGAUUCAGAAAAUAACGGGAGAGGUGAAAAUCCAUGAUCGCUAUAAGAUGCACGAGAGCGAAAGCAUUUCACUCAACUGUGUCCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCCUAACUAUAAACGAUGUCAACCAAGGAUUGGAUGAAAUUCAGAUGUACAAAGAUAGAGAAGCAUUGUUUCUAGAUCUGAGUAUAUCAAUAUUACCUUGUUCAGAACUUAAAGAGAAAUCUUGAGUUUAUGGACUUCAGGGGGAGUAUGGUCACAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACACCAGGAGUGGAGCCUGCGCUUAAUUUGACUCAACACGGGAAAACUUACCAAGACCGAACAGUAGAAGGAAUGACAGAUUAAGAGUUCUUUCAUGAUUUAUUGGGUAGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCAGGUUAAUUCCGGUAACGAACGAGACUGAAACCUAUUAAUUAGUUUUCUGCCUAUAAGACAGAAAUGUUCGCAAGAACAGGUGCGUAAGUACCACUUCUUAAAGGGACACAUUUCAAUUGUCCUAUUUUAAUUGUAGUUAUCUAAUUUCGGUUAGACCUCUUUUAACGUGGGAAAAAGAAAAAGGAAGCAUUCAGCAAUAACAGGUCUGUGAUGCCCUUAGACAUCUUGGGCCGCACSCSCGCUACAAUGGAGUUACUAGAGAGUAUUUUAUCAUUUACACCUUAUUUAUUAGGCUUUGUCUAAUAAUUAAGGAUAGUAAGUGGUGUACCGAGAUUGAAAUAGUUAAGGAAAACUCAAAAGAACGUACAUGACAGGGAUAAAUGAUUGGAAUUAUUUGUUUUGAACGAGGAAUUCCUUGUAAUAUCGAGUCAUUAACUCGAGAUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUAAAGAGGUGAAAUUCUAGGAUUCUGUCUUAUAGAUAGAAAAAUGGAUUUAAAUCUCCUUAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq new file mode 100644 index 0000000..ca7e6aa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.mobilis.seq @@ -0,0 +1,2 @@ +>d.16.e.E.mobilis +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUGCGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGAGGGCUCCAAUGUCCGCUGAUGCGUGUGCAGCGGAGCCCUCUCAUCCUUCUGUUAACGUUUCUUGGUAUUCAGUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUUCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUAUUGUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAGCCAAUCCCGAUUGGCCCCGACUUCUUAGAGGGACUUUGUGAUUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGCGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGGACAUCCUCGUGGUGUUUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq new file mode 100644 index 0000000..69b8094 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.E.schubergi.seq @@ -0,0 +1,2 @@ +>d.16.e.E.schubergi +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAGUCUCUGAGAUUAAGCCAUGCAUGUCUAUGGAACAAGGACGAACAGCUCAGUAAAACUGCGAUGAUUCAGUCUGUCUGUCAAGAUAACCACGCGAAAGUGUGGCUAAGAGGGGACAGAACAAGACGCAGGACUAUCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACGGUGACGGUUGACGGGGAAUGAGGGUUCUAUACCGGAGAGGGAGCCUGAGAGAUAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUGUUUGGAGGAGGCAGUUAUGAGACGUGAGAAAGAGUGCUUGUAAAGAGAAGCAGGAGAAUUGGAGGGCAAGUUUGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGUAGUCGUGGAGACGGAAAGAGAGGCGGAGCCUCUUUGAGAUGCUCUGGAGAAGCCAACAGGGGGCACAGUAUACCAGGGCGAGAGAUGAAAUGCCAAGACCCCUGGUGGACUGAGCGAGGCGAAAGCGGUGCUCUUGUGGGUGUUCGGUGAUCAAGGACGAAGGCUGGAGGAUCGAAAGUGAUUAGAUACCGCUGUAGUUCCAGCAGUAAAAGAUGCCGACAUGCUCGGUGGCAACACGGGGCAGGGAGAAAUCUUAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGGGUGAAAAUUAAAGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGAAGCUUACCAGGGCCAAGUGCUGUGGAGAAAGGAGCAGUACAGAAGUGGUGCAUGGUCGUUGGAAAUUGAUGGGAUGACUUUGGCCUUAAAUGGCUGAAUGAGUGAGAUCUUUGGACAUGUUCCCACGGAACAGGAAGGGGAGGCUAUAACAGAUCAGAGAUGCCCUUAGAUGCCCUGGGCUGCACGCGCAAUACAAUAGCACGUAGACGUAGAGAACAACACGUGCUGAGGUGGACUGUGCUCUGCAAGGGGCACACGAAAGAGGAAUUCCUAGUAAGCGCCCAUCACCAGUGGGCGUUGAAUCAGUCCCUGUAGCUUGUACACACCGUCCGUCACUAUCUCAGAUGUUUUUCGGGAUGAAGAGUCCAGGCUCUGAAUAACGGAAAGUAGAUAAGAUGUAAGUCGUAGCAAGGUUGCGGUCGGUGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq new file mode 100644 index 0000000..a4c4989 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Encephalitozoon.sp.seq @@ -0,0 +1,2 @@ +>d.16.e.Encephalitozoon.sp +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUGUUCUCUGGGACUAAGCCAUGCAUGUUGAUGAACCUUGUGGGGGAUUGACGGACGGCUCAGUGAUAGUACGAUGAUUUGGUUGGCGGGAGAGCUGUAACUGCGGGAAACUGCAGGUAGGGGGCUAGGAGUGUUUUUGACACGAGCCAAGUAAGCUGUAGGCCUAUCAGCUGGUAGUUAGGGUAAUGGCCUAACUAGGCGGAGACGGGAGACGGGGGAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUUUGGGGAGGCGGUUAUGAGAAGUGAGUUUUUUUCGAGUGUAAAGGAGUCGAGAUUGAUUGGAGGGCAAGUCGCGUGCCAGCAGCCGCGGUAAUACCUGCUCCAAUAGUGUCUAUGGUGAAUGCUGCAGUUAAAAAGUCCGUAGUCUUUUGUAUGUCUUUGUUUGGGGGAUUAUGUCCUGAUGUGGAUGUAAGAGGUUUGGCAGAGGACGAGGGGCACCGGAUAGUUGGGCGAGGGGUGAAAUACGAAGACCCUGACUGGACGGACAGAAGCGAAGGCUGUGCUCUUGGACUUAUGUGACGAUGAAGGACGAAGGCUAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUAGCAGUAAACGAUGCCGACUGGACGGGACUAUAUAGUGUUGUGCAUGAGAAAUCUUGAGUAUGUGGGUUCUGGGGAUAGUAUGCUCGCAAGAGUGAAACUUGAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCGGUUCUGAAGCGGGCAGGAGAACGAGGACGGGAUGCGUGCGGCGGUGGUGCAUGGCCGUUUGAAAUGGAUGGCGUGAGCUUUGGAUUAAGUUGCGUAAGAUGUGAGACCCUUUGACAGUGCUCUUUGGGGCAAGGGAGGAAUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGAAGCGGGCGGCACGCGCACUACGAUAGAUGGCGAGGGAGCCUGCUGUGAGGGAUGAAGCUGUGUAAUGGGCUUCUGAACGUGGAAUUCCUAGUAAUAACGAUUGAACAAGUUGUUUUGAAUGGGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCCAAGAUGACGCAGUGGACGAAGAUUGGAAGGUCUGAGUCCUUCGUGUUAGAUAAGAUAUAAGUCGUAACAUGGCUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq new file mode 100644 index 0000000..1b84530 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.F.x.ananassa.seq @@ -0,0 +1,2 @@ +>d.16.e.F.x.ananassa +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAAUCCCGACUUCUGAGAAGGGAUGCAUUUAUUAGAUAAAAGGUCAACGCGGGCUCUGCUCGCAUUGAUGAUUCAUGAUAACUCGACGGAUCGCACAGCCUUUGUGCUGGCGACGCAUCAUUCAAAUAUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGUUGGGUCGACCGGUCCGCCUUAUGGUGUGCACCGGUCGGCUCGUCCCUUCUACCGGCGAUACGCUCCUGGCCUUAACUGGCCGGGUCGUGCCUCCGGUGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGGUCCUAUUCUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUACUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUCGGGAGGUCUCCUCGGGCCAGCUUCUUAGAGGGACUAUGGCCGCUUAGCGAACCAAGUUUGAGGCAAUAACAGGUCUGUCAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUCUAUAGCCUUGGCCGACCACGGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUUGUUCGGAUCGCGGCGACGGGGGGCCGGUUCGCUGCCCGCGACGUCGCGAGAAGUUCCACUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq new file mode 100644 index 0000000..4d70b84 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.intestinalis.seq @@ -0,0 +1,2 @@ +>d.16.e.G.intestinalis +CAUCCGGUCGAUCCUGCCGGAGCGCGACGCUCUCCCCAAGGACGAAGCCAUGCAUGCCCGCUCACCCGGGACGCGGCGGACGGCUCAGGACAACGGUUGCACCCCCCGCGGCGGUCCCUGCUAGCCGGACACCGCUGGCAACCCGGCGCCAAGACGUGCGCGCAAGGGCGGGCGCCCGCGGGCGAGCAGCGUGACGCAGCGACGGCCCGCCCGGGCUUCCGGGGCAUCACCCGGUCGGCGCGGUCGCGGCGCGCCGAGGGCCCGACGCCUGGCGGAGAAUCAGGGUUCGACUCCGGAGAGCGGGCCUGCGAGACGGCCCGCACAUCCAAGGACGGCAGCAGGCGCGGAACUUGCCCAAUGCGCGGCGCGCGAGGCAGCGACGGGGAGCGCGCGAGCGAGGCGGGCCCACAGCCCCCGCCGCGGAGCCGAGGGCAAGGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCGGCGAGCGUCGCGCGGCGCUGCUGCAGUUGAAACGCCCGUAGUUGGCCCCCCGCCGCCACGAGGAAACGGGAGCGCUCCAGGCAGGCCCGUUGGACCCGCCGCGUGGGACCGCGCAGCGGGCCGGCGCGCCGCGGCAGCCCCGAGGAGAGCGGGCGGGGGCACCGGUACCGGCCGGGGACGGGUGAAACAGGAUGAUCCCGCCGAGACCGCCGGCCGCGCAGGCGCCUGCCAAGACCGCCUCUGUCAAUCAAGGGCGAAGGCCGGGGGCUAGAAGGCGAUCAGACACCACCGUAUUCCCGGCCGUAAACGGUGCCGCCCCGCGGCCGGCGCGCGCGUCCCGCCGGCCGCCCAGGGAAACCGGGAGGCUCCGGGCUCUGGGGGGAGUAUGGCCGCAAGGCUGAAACUUGAAGGCAUUGACGGAGGGGUACCACCAGACGUGGAGUCUGCGGCUCAAUCUGACUCAACGCGCGCACCUCACCAGGCCCGGACGCGCGGAGGACCGACAGCCGGGCGCGCUUUCGCGAUCGCGCGGGCGGUGGUGCAUGGCCGCUCCCAGCCCGUGGCGCGAGCCGUCUGCUCCAUUGCGACAACGAGCGAGACCCCGGCCGCGGGCGCCGCGGGACGGCCCGCGCGAGCGGGAGGACGGCGGGGCGAUAGCAGGUCUGUGAUGCCCUCAGACGCCCUGGGCCGCACGCGCGCUACACUGGCGGGGCCAGCCGGCGCGCGCGAGGACGCGCGGAGCCCCCGCCGUGGCCGGGACCGCGGGCUGGAACGCCCCCGCGCACCAGGAAUGUCUUGUAGGCGCCCGCCCCCACCGCGCGCCGGACGCGUCCCUGCCCCUUGUACACACCGCCCGUCGCUCCUACCGACUGGGCGCGGCGGCGAGCGCCCCGGACGCGCGAAGGGCCGCGAGCCCCCGCGCCUGGAGGAAGGAGAAGUCGUAACAAGGUAUUCCGUAGGUGAACCUGCGGAUGGAUCCCUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq new file mode 100644 index 0000000..6e4347c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.max.seq @@ -0,0 +1,2 @@ +>d.16.e.G.max +UACUUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACUAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCAACACAGGCUCUGCCUGUUGCUUUGAUGAUUCAUGAUAACUCGUCGGAUCGCACGGCCUUUGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCAUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAUGGAUCCAUUGAAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGUUGGGUCGAUCGGUCCGCCUCCGGUGUGCACCGGUCGGCUCGUCCCUUCUGCCGGCGAUGCGCUCCUGUCCUUAACUGGCCGGGUCGUGCCUCCGGUGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACACCACAGGAUUCUGAUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUUUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAAAUAGCUAUGUGGAGGUAACCCUCCACGGCCAGCUUCUUAGAGGGACUAUGGCCGCUUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGUCUAUAGCCUUGGCCGACAGGUCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUUGCGGCGACGUGAGCGGUUCGCUGCCCGCGACGUUGUGAGAAGUCCACUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq new file mode 100644 index 0000000..2188860 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.steinii.seq @@ -0,0 +1,2 @@ +>d.16.e.G.steinii +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCGAUGUCGUCUUGUUGAUUGUGCAGAGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCAGAGGCGCGCUUUAUCCGCCUUUGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGCUUAGCGGACACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACCGCGGAGUUCUCGUAAUUCUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq new file mode 100644 index 0000000..7343a20 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vagum.seq @@ -0,0 +1,2 @@ +>d.16.e.G.vagum +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAACUCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAGGCAACUUUUGUCGUGGUAUAAAUUGGAGAUACAAACCAAUAUUUGGUGAUUCACGAUUUCUUUUCUGAUCGCACUAUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAACUUGGCGGGCGACGCAGGGCGUCUUUGCGGACGGUUCUGUAUCGGCCGCCUUUGUGGAGGGGGGCUUAGCGGUGCUUUAUUGCCUUGCUAAGUCGCUGCCACCGUUUACUGUGAAAAAAUUGGAGUGUUCAAAGCAGGCGUUUGCCUUGUACACAUUAGCAUGGAAUAAUAGAAUAGGACCUGGUUCUGUUUUGUUGGUUUGUGAGAAUUAGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCUGCCGUCAGAGGUGAAAUUCUUAGAUUGGCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGGCGCUGCUUUAUGGCCCGCCCGGCACCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCGUUACCUCUUUCGGUAGCGAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUAGGCGAGAGCCUUUCCUAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGUCGGACUGUGUUUUACAGACCAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGACCCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq new file mode 100644 index 0000000..acaa018 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.G.vavrai.seq @@ -0,0 +1,2 @@ +>d.16.e.G.vavrai +CACCAGGUUGAUUCUGCCUGACGUGGACGCUUGCCUUAAAGAUUAAGCCAUGCAAGCCAGCGAAGGUAACGGAGCGGCGAACGGCUCAGUAGGACAGGGUUAUCUGACCACCGAACAGGAUAACCGCGGUAAUCUGUGGCUAAUACGUGUGUGGGUGAGACUCUGCCCUAUCAGCUUGGGGGUACGGUAAGUGCGUACCCUUGCGACGACGGGUAACGGGAAAUCGGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCACGUCCAAGGAUGGCAGCAGGCGCGGAAAUUACCCACUUGGAGGACCAGAGGUAGUGACGAGGCGUUUUUAAUGAGAAUAGUGUAAAAAGCUGUUCGAAAGCAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGAGCGUCUGCGUGUGUUGCUGCGGUUAAAGAGUGCGUAGUCGGGUUAUUUGCCAGCAAUAAAGGUGCAGUCUCUAACUGUAUAUUGUGCUGGUACUUUGAUCUAGGAACUGGAUAAAGGUUAUGGUAUUCGACAGCGAGGGGUGAAAAUUAAUGACCUGUUGAGGAGCGACUGAUGCGAAAGCGGUAAUCUAUGACGGGUUUGACGAUAAAGCGCGUAGGCAGGAGUAUCGAAGGCGAUUAGAGACCGUCGUAGUUCUUUGCAGUAAACGAUGCCAACAGGAAUGCAAGUGCUGUGUUCCUAGGGAAACUGAGUGUAUGGGCUCUGGGGAUAGUACAGGCGCAAGCUAGAAACUUGAGGAAAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGACAACUUACCAGGGUAUGUGACAUUGAGCGAAGAGCAUGGAUGCGAUCUGUGUUCUGAUGAUGUUACGUGUGGUGCAUGGCCGUUCUUAACACGUGGGGUGACCUGUCUGGUUAAAUCCGAUAACGCGUGAGACCCUGGAUAAUGACGAUACUUGACAAGAGUAGGGAAGCUCGGGUCGAUAACAGGUCUGUGAUGCCCAUAGAUAUUUUGGGCGCCACGCGCACUACAUUGGGGAUGGUUACGUGAAACGGAACAUCCUUUCGGUUGGGAUUGACGUUUGUAAAUACGUCAUGAACUCGGAAUUCCUAGUAAUUUGUUGUCAUUAACGACAUAUGAAUAUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGAAUGUGCGGAUGAAGUUGGUUAGGUCAAAAGAAUCCGUGCGAUUAGAUUGGAUACAAGUCGUAACAAGGUUACUGUAGGAGAACCUGCAGUAGGAUCAAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq new file mode 100644 index 0000000..78438aa --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Gracilariopsis.sp.seq @@ -0,0 +1,2 @@ +>d.16.e.Gracilariopsis.sp +CAACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUAUAGGACUAAGCCAUGCAAGUGCAAGUAUGAGUGUAUUAUACAACGAAACUGCGAAUGGCUCUGUAAAACAGCUAUAAUUUCUUCGGUGCUAAAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCUACACAGCGACGCAAGUCGUGGUACAAAUUAGAUACACAAGCCAGCUUUUUUGGUGAUUCUAGAUUUUUUUUCUGAUCGCACAUUGUUGCGACGCACCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAAUGGCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAACUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGAUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAAUUUUGGCGUGUGAUUUGGGUCGUUCUCGCGGACGCGCUCAGGUUGUGCGCCUUUGUGGAGAGGGGGUGUGGUGGUGCUUGAGUGCGCUGCCAUGCUGCCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGAUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCCGGUUCUAUUUUGUUGGUUUGUUUGAAUCAGGUAAUGAUUAACAGGGACGGUUGGGGGCAUUCGUAUUCCGGCGCUAGAGGUGAAAUUCUUGGAUUGUCGGAAGACGAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGACAAGACUGAUUUAUGGCUUGUUCGGCAUCCUUCGAGAAAUCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCCGUUACCAAUUGAGUUUGGUAGCGAGGCGGUGCCUUCCUAGACGGACUGUGGGCGUCUAGCCCACGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAACGGCCCAACGAGUGGAGGAUGUGCGAGAGCAUUUCCGAAUCUCCAAAUCCGUUCGUGAUGGGGAUCGACGGUUGCAAUUUUCCGUCGUCAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUGGAUGCGCUGUUUUUAUGCAGACAUUUUGGCCUGAACCUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq new file mode 100644 index 0000000..9c2f96f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.anguillarum.seq @@ -0,0 +1,2 @@ +>d.16.e.H.anguillarum +CACCAGGUUGAUUCUGCCUGACGUGGACGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAGGCGAAGCAUUUUGUGGAGCGGCGGAAGGCUCAGUAACGGGCGUCUAUUUGAUCUUCUGAGACGGACAACCUCUGUAACCGGAGGCCAAUACGUCAGAGGCACGGUUACCCUGUGUGGUGGUGUGCCGAAAGCAUUGCGCGGAAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUGUGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCGGUGAGGGCGGUAGUAAGGAGACGUGGAAACGAUGAGGAGGUAAAGAAUGCUCUGGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGGCUGCGUGACUGGCGUGAAAGGCCUUCUUUCAAGGGGGGCACAGCGCGGGGAAAGCAGAGGAUAAGGAGCGUUUUGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGGAACAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGUGCGUGCGCGCGACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGACCGCACGAGUGUUGUACACGAUAGGUCGAAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCUGUCCGGCAGACAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGCGUGGGCUGCACGCGCACUACAGUGGUCACAGAAAGAAUCGCGGAGAGACAAUGGUGAUCGAGAGGGAAUGAGCUUUGCAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCUGUAGCUGGAUCAGCG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq new file mode 100644 index 0000000..4d623b3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.plana.seq @@ -0,0 +1,2 @@ +>d.16.e.H.plana +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUAAACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCCUAAGACGACGCAAGUCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACGAUUUCUUUUCUGAUUGCACUUUUGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAGUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGAAAUUUGGCGGGCGACUUAAGUCGUCUUUACCGACGAUCUUAGGUUGGCCGCCUUUGUGGAGGGGGGCCUAGUGGUGCUUAACCGCUUCGCUAGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCCUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUUCUAUUUUGUUGGUUUGUUAGGAUCGGGUAAUGAUUAAGAGGGAUGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGUUGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACAUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGCGGGGCUGUUUUUGGCCCGCCCGGCAUCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGGAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGUUAGCUAGGCGCCAUUACCCCUUUUGGUAGUGAGGCUAGCCUUCCUAAACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGUGAGGAUGUGCGAGAGCGCUUCCCAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGCGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGAUAGUCGGUGUUUUCACAGAUCAUCUGGCCCAAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq new file mode 100644 index 0000000..734e464 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.rubra.seq @@ -0,0 +1,2 @@ +>d.16.e.H.rubra +CAACCUGGUUGAUCCUGCCAGUGGUAUAGUCUUGUCUCAAGGACUAAGCCAUGCAAGUGCCAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGGGGGUAAUACUACCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCCGAAAGCGAGUCUCUCGCGGUACAAAUUGGAGACACAAGCCAAUAUUUUGGUGAUUCACAAUUUUUUUUCUGAUUGCACUUUUUAGUGCGACACCCCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAYUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUACUAAUUCAGUGAGGUAGUGACAAAGAGUAUCAAUAGGGGGGCCAUCGGCUCUUCUAGUUGGAAUGAGUACAGAGUAAACAAUUUAACGAGGACCAAUAGGAGGGCAAGCCAAGUGCCAGCAGCCGCGGUAAUACUUACUCCUAGGGUGUUUGUUCACAGUGCUGCAGUUAAAAAGUUCGUAGUCGGACCUAUGAGCUGGGCGGUGGUGUGGGCGCAAGCCUGUGGUGCCGCCCGGCUCUUUUGGGGAAAUGGCCGGAGUAGGGUUUUAAGCGGCUUUGCUCCGGGCGUCCCCCGUUUACUGUGAAAAAAUGAGAGUGUUCAAAGCAGGCGAUGAGCCGUGAAUACCAUAGCAUGGAAUAAUAGAAUAGGGCCGCUGAUGCCUAUUUUGUUGGUUUCGAGGUGUCGGGCAAUGAUUAAGAGGGACGGUUGGGGUCAUUUGUAUUAAGUCGUCAGAGGUGAAAUUCUUAGAUUGACGUAAGACAAACAGCUGCGAAAGCGUCUGACAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUAAGAACUGGGGAUCGGAAGAGUAUUUAAAUAGGGCUCAUCCGGCACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAGUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGAGCGUGGUAGCUAGGGGACUUGUGCAUUUAUGCACGGGCUUUUUCUCCUUCCUACACGGACUGCUGGCGAAUAGUCAGCGGAAGCCUCAGGCAAUAACAGGUCUGUGAUGCCCUUUGAUGUUCUGGGCCGCACGCGCGCUGCACUGAGCGGACCAGCGGGCGAGGAUAGCCGAAAGGUUUUCCGGACCCUUAAAUUCGCUCGUGCUGGGGAUGGAGGCUUGCAAUUGUCCCUCUUGAACGAGGAAUACCUUGUAGGCGUGAGUCAUCAGCUCGCGCCGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGGGUGAGGAGGUGAGAAGUUGGGAGGUGUUGGUUCGGGCCCGCAAGGUGUCUGGGCUAGCGCUAAACUCGUUCAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAGAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq new file mode 100644 index 0000000..c04feb9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.H.sapiens.seq @@ -0,0 +1,2 @@ +>d.16.e.H.sapiens +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCUUCGCGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCCCUCUCCGGCCCCGGCCGGGGGGCGGGCGCCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACCGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq new file mode 100644 index 0000000..f212fda --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.I.hoferi.seq @@ -0,0 +1,2 @@ +>d.16.e.I.hoferi +CAACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAACAACUUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUAAUACCUACUACUUGGAUAACCGUAGUAAUUCUAGAGCUAAUACAUGCGAAAAAACCCGACUUCUGGAAGGGUUGUAUUUAUUAGAUACAGAACCACUGCAGGGCAACCUGGUUACUUGGUGAUUCAUAAUAACUUCGCGAAUCGAAUGGCUUGUGCCGUCGAUGAUUCAUUCAAAUCUCUGCCCUAUCAACUUUCGGUGGUAAGGUAUUGGCUUACCAUGGUUCCAACGGGUAACGGAGAAUUAGGGUUCGAUUCCCGAGAGGGAGCCUGAGAAACGGCUACCACUUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAAAAAUAACAAUACAGGAUCUUUAAAGGUCUUGUAAUUGGAAUGAGUACAAUUUAAACCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUUGGAAAUUGCUUACUGGUCGGCCGCAAGGUCUGUACUGGUACGGCAGUUUCUUCUUCUCGAAGGCAGUGGGUGCUCUUAAUUGAGUGUCUACUGAGUUCGGGACUUUUACUGUGAGAAAAUUAGAGUGUUCAAAGCAGGCUUAUGCUUGAAUAUUGCAGCAUGGAAUAAUGGAAUAGGAUCCCGAUCUUAUUUUGUUGGUUUCUAAGAUCGAGAUAAUGAUUAAUAGGGACGGUUGGGGGCAUUAAUAUUUAAUUGUCAGAGGUGGAAUUCUUGGAUUUAUGAAAGAUUAACUUCUGCGAAAGCAUUUGCCAAGGAUGUUUUCGUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCAUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUUAGUGGACGUUUAAUAAUGACACCAUUAGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCCCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACCAGGUCCGGACAUAGGAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGCCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUACUAAAUAGUUACAUGAUUUUCGAAUCAUGGGCAACUUCUUAGGGGGACUAUUGGUGUAUAAUCAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGAGGUCAACGAGUAUCAUCCUUCACCGGAAGGUGCGGGUAAUCUUUUGAAACCUUAUCGUGAUGGGGAUAGAUCAUUGCAAUUAUUGAUCUUCAACGAGGAAUUCCUAGUAAGCGUGAGUCAUCAGCUCGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGUUUAGUGAGGUCCUCGGACUGGUACAGCGCGUGGCAACACAUACUGCGCCGGGAAGUUGAACAAACUUGAUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCUAGU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq new file mode 100644 index 0000000..aea2f0f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ichthyosporidium.sp.seq @@ -0,0 +1,2 @@ +>d.16.e.Ichthyosporidium.sp +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCUAAAGUUAAGCCAUGGAUGUCUAAGCAAAGCGUAAGUCGAGCGGCACAGGCUCAGUAACGGGCGAAUAUUUAAUCUCCUCGAGUGGAUAUCCUCUGUAACCGGAGGGCAAAACACAGGACGUGCAGUUGUAUAAGGAUUGUUCGUUUAACAUUAGUGGGGGAGAGUAAGACGCCAGUCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAUACGGAUACGGGGAAUUAUCGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCGGGUCCAAGGACAACAGCAGGCGCGAAAAUUACCGCAGCCUGCAUUCAGGUCGGUAGUAAGGAGACGUGUAAACGAUGUGCAGGUAAAGAAUGCACUGUAUACAGGAGGACAAGACUGGUGCCAGCACCCGCUGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGCGUUCGUAGUCGAACCGGGUUGAAUUGCGUGACAGUCAGACUCUCAAGGUGUGAUGAGCGCUGUGAUUCUGGGGAAUAAGGAGUGUUUAGGGGCCAGGGUAUUAAACGGCAAGCGGUGAAAUGUGUUGACCCGUUUAUGGAGCGACAGAGGCGAAAGGCUGGCCAGGGGCAAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACAAUGCCGAUGUUGUGGUGCCGUAACGGACGCAAAAGAGAAAUCUAGUAGGGCCCUGGGGAGAGUACACGCGCAACAGGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACACCUUACCGGGCCCACGGCCACACGAGUGUGACACACGAUAGCCGAGGAGUGGUGCAUGGCCCGUUAACGACAAGUGAGUGAUCUUUGGGUUAAGUCCGUAAAUUAGUGAGACCCCAGCAAAGGACAGGUGCGCAAAGCACAGGAAGGAUGGGUCAAGGACAGGUCAGUGAUGCCCUUAGAUGGUCCGGGCUGCACGCGCACUACAGUGGUCGCCGAAAUUUAGAUAUAGAGCUAAAGGCGAUCGAGAGGGAAUGAGCUUUGGAAGAGGCUCAGGAACGUGGAAUUGCUAGUAAUCGCGGACUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAUACGGUGCUCGGCGCGAGCAAGGUGAAAUCACUGAGCGAGCGCAAGGUACCGGAUCUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq new file mode 100644 index 0000000..0970601 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.J.debaisieuxi.seq @@ -0,0 +1,2 @@ +>d.16.e.J.debaisieuxi +CACCAGGUUGAUUCUGCCUGACGUAUGUGCUUGUCUUAAAGAUUUAGCCAUGCAAGUUAGUGAAACUUUUUAAGUGAAACGACAGACAGCUCAGUAAUACAGUAAUGAUUAACUUGCCUAAUAUAGGAUAACCUUGGUAACCUAAGGCUAACACUUUUUUCAAAUUAAAAUGUAGGUGAAACUAUUUUUAAUUUUUUUUUGGGGCAAUUAAGUUUCUGACCUAUCAGCUAGAUGUUAGGGUAAAGGCUUAACAUGGCUACAACGGGUAACGGAGAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAAUUAGCUACCACGUCUAAGGAUGGCAGCAGGCGCGAAAAUUACCCAAUUCCUUAAUGGGAGAGGUAGUGAAAAGACAUGAUUUUCAUUUCGAUUGAGUCGGUACAUUAAAUAAGUACUGAAGCAACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAAUAGUUGCUGCAGUUAAAAUGUCCGUAGUUGAUUUAAUUAAACUGUGAGUAAAUUAUAGAGCUCAAAACUAUAAGUAAGCAUGGUAUUAUAAGAUAAUAGGAACAGAUGAUGGCAAUAGUAUUCAAUAGUUAGAGGUGAAAAUUUAAGACCUAUUGAGGACUACCAGAAGCGAAAGCGAUUGUCAAGGAUGUCUCCAUUAAUAAGGGACUUAAGCUAGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCUAGCUGUAAACGAUGCCUACUAGGUGAUGUUUAAAUGGCUAUGCCUUAGGAGAAAUCAAAGUCUACGGGCUCUGGGGAUAGUAUACUGGCAACGGUGAAACUUAAAUGAAAUUGACGGAAGAAUACCACGAGGAGUGGAUUAUGCGGCUUAAUUUGACUCAACGCGGGACAACUUACCAGAGCCGAACCUGUAUGAGAAUUUAUAAUGUAAAUGAUAAUAGGGAAGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACUUGUCAGGUUAAUUCCGAUAACGCGUGAGGUUUAUUAAAUAAUUGUUUAUUUGACGGAUGAUAAGAAAUCAUAGGAAGUUAAGCUAUAACAGGUCGGUGAUGCCCCUAGAUGUUCUGGGCUGCACGCGUACUACAAUGAUAUAUUUAAUAUUAAUAUUGAGAAAUAUAACUCUAAUAUAUAUCGAAGCUGGGAUAAGCUAUUGUAAAUUAGUUUUGAACUUGGAAUUCCUAGUAAUCAUAAGUCAUUAUGUUAUGAUGAAUGCGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUAAGAUGGAUGUAUAGGUGAAAUGGCUAGACGUAAAUGGAAAGCAGUUAACCUGUGCAACUAAUAGGAUAUAAGUCGUAACAAGGCUGCUAUAGGUGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq new file mode 100644 index 0000000..b74a2ea --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.L.acerinae.seq @@ -0,0 +1,2 @@ +>d.16.e.L.acerinae +CACCAGGUUGAUUCUGCCUGGUGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAAGCAAAGCUAGAAGUGGAGCGGCGCAAGGCUCAGUAACGGGCGGACAUUUGAUCUUCUCGUGUGGACAUCCUCUGUAAGCGGAGGGAAAAACACAGGACGCGCGGACGCAGCCCGUGGGUGUAACGGCGGUGGAGAAGAGUAAGACGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUGAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGCAGCCUGCCUCAGGGCGGUAGUAAGGAGACGUGAAUGCGAAGUGCUAGCAAAGAAAGCACUGACAACAGGAGGACAAGACUGGUGCCAGCACCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGGGUUCGUAGUCUGAGCGGAACGAGGGGUGUGACGGGUCCCAGCUCAAGGGGGACAUAGCACCGCGAUGCCGCGGAACAAGGAGCGUCUAGGGGCCAGGGUAUUAAGCGACGAGGGGUGAAAUCUGGUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGGCCAGGGGCGAGUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGUGCCGCAAGGCGACGCGGAAGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGUCCCGACGAUCGGAGGAGUGUGUUACACGAUAGGUCGGAGAGUGGUGCAUGGCCGUUAACGACGAGUGGGGUGACCUUUGGGUUAAGUCCGUGAAGUAGUGAGACCCCUGCCGCAAGGGACAGGUGCCGAACGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUCAGAUGGGCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAAGGAAGGAAAGAGAUAAAGGCGAUCGAGAGGGAACGAGCUUUGGAAGAGGCUCGGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAGGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq new file mode 100644 index 0000000..1e52f3a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.musculus.seq @@ -0,0 +1,2 @@ +>d.16.e.M.musculus +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCCUUCCCGGGGGGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUGAGCUCCCUCCCGGCUCCGGCCGGGGGUCGGGCGCCGGCGGCUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCCCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGUCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUGCGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq new file mode 100644 index 0000000..93e0dc2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.M.racemosus.seq @@ -0,0 +1,2 @@ +>d.16.e.M.racemosus +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAAUAAAUUUAUAUUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGAUCUACGUGACAUAUUCUUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAACCCAAACUUACGAAUGGGUGCACUUAUUAGAUAAAGCCAACGCUGGGUAAAACCAGUUUCCCUUGGUGAUUCAUAAUAAUUUAGCGGAUCGCAUGGCCUUGUGCUAGCGACAGUCCACUCGAUUUUCUGCCCUAUCAUGGUUGAGAUUGUAAGAUAGAGGCUUACAAUGCCUACAACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUGCAGGGCCUUUAAGGUCUUGCAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAACGUCCGUAGUCAAAUUUUAGCCUUUAGAUGAGGUGGCCUGGUCUUCAUUGAUCAAGCUCGCUUUUAUCGAGGCUUUUUUUCUGGUUAUGCUAUGAAUAGCUUCGGUUGUUUAUAGUCUCUAGCCAGAUGAUUACCAUGAGCAAAUCAGAGUGUUUAAAGCAGGCUUUCAAGCUUGAAUGUGUUAGCAUGGAAUAAUGAAAUAUGACUUUAGUCCCUAUUUCGUUGGUUCAGGAACUUAAGUAAUGAUGAAUAGAAACGGUUGGGGACAUUUGUAUUUGGUCGCUAGAGGUGAAAUUCUUGGAUUGACCGAAGACAAACUACUGCGAAAGCAUUUGAUCCAGGACGUUUUCAUUGAUCAAGGUCUAAAGUUAAGGGAUCGAAGACGAUUAGAUACCGUCGUAGUCUUAACCACAAACUAUGCCGACUAGAGAUUGGGCUUGUUUAUUAUGACUAGCUCAGCAUCUUAGCGAAAGUAAAGUUUUUGGGUUCUGGGGGGAGUAUGGGACGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAAAGCUCUUUCUAGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUCGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUAUUCUGCUAAAUAGGCAGGUCAACUUUUUAGUUGAUUAAUAGAUUUAUCUAUCUGGCUUCUUAGAGAGACUAUCGGCUUCAAGCCGAAGGAAGUUUUAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGAAAUCAGCGAGUUUAUAACCUUAGCCGGAAGGUUUGGGUAAACUUUUGAAAUUUCAUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGUUAUAGUGAGCAUAUGGGAUCAGUAGAAUUAGGUUGGCAACAACCUUUCUCUGCAGAGAACUAUGGCAAACUAGGCUAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq new file mode 100644 index 0000000..100309a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Microsporidium.sp.DP119.seq @@ -0,0 +1,2 @@ +>d.16.e.Microsporidium.sp.DP119 +CACCAGGUUGAUUCUGCCUGGUGUAGAUGCUAGUUUCUAAGAUUUAGCCAUGCAUGUUUUGUGAAUUCUUACGAAGGAACGGCGAACGGCUCAGUAAUAUUGCGUUAAUCUGGUCUAAAUAUAAAAAUAACUACGGUAACCUGUAGCUAAUAAUUUAGAAUGAGACGCAAAUUUAUCAGUUUGUUGGUAGUGUAAUGGACUACCAAGACUAUGACGAAUAACGGGAAAUUAGGGUUUUAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGUCCACUCUUUUAUGAGGAGACAGUUAUGAAACGUGAAUAUAAGUUUGAAUUUUAAAAUAAUUUAUUUUAUGCAAUUGGAGGGCAAGUUUUGGUGCCAGCAGCCGCGGUAAUACCAACUCCAAGAGUGUCUAUGAARGUUGCUGCAGUUAAAGCGUCCGUAGUUUUUUUAUUGCAAUUUAAAAACUAUGAUUAAAUUAGUUAAGUUUCCAAUACAUUGUGAAACGGAUAGGGAAAAUUGUAUAGCUAGGUGAAGAAUGAAAUCUCAAGACCCUAACUCGACAAACAGAGGCGAAGGCGAUUUUCUUAUACGUAUUCUUAAAUAAAGGACGAUAGUUAGAGGAUCGAAGGUGAUUAGAGACCGCUGUAGUUCUAACUGUAAACUUUGCCGACAUUUCAUAUUGUUUUGAUAAGAAAGGGAGAAAUCUUAGUUUUCGGGCUCUGGGGAUAGUACACUCGCAAGGGAGAAACUUAAAGCGAAAUUGACGGAAGAACACUACCAGGAGUGGAUUGUGCUGCUUAAUUUGACUCAACGCGGGAAAACUUACCAGAGUCAAAUAUAUUUAUGAUUUUUUUAAAUGAAAUAUAUAAAAGUGGUGCAUGGCCGUUGCAAAUUGAUGGGUUGACUUUUAACUUAAUUGUUGAAACCAGUGAGAUCAUUUAUGACUGGUAUUUUAAAUACAGGAAGGAAAUGGCAAUAACAGGUCCGCACGCCCUUAGACAUUCUGGGCUGCAAGCGCAAUACAAUAUCUUGUUAUUUAUAUUUAUUUAUACAAUUAUAUGUAGGAUUAAUUCUUGUAAAUGAAUUAUGAAUCAGGAAUUCCUAGUAAUAAUAUUUCAUUAAGAUAUUAUGAAUUUGUCCCUGUUCUUUGUACACACCGUCCGUCACUAUUUCAGAUGGUUAUAAAGAUGAAGAGCUAAGGUUCUGAAUAUUUAUAACUAGAUAAAGUACAAGUCGUAGCAAGGUUGCAGUCGGUGAACCAUCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq new file mode 100644 index 0000000..6ff328d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.colligata.seq @@ -0,0 +1,2 @@ +>d.16.e.O.colligata +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUGUCUGAGAUUAAGCCAUGCAUGUGAGUGAAUGUAGUAAGCAGGAACUGCGGACGGCUCAGUAAGACUACGAUGAAAUGAUCUGCGAAGAAGAAGUAACGGCGGGAAACUGAAGAAGAGAGUUUUUGAGAAUACUUGAAGGGAUGCGGAGAAGUGAUUUUUGAAGUGAUGUUGAGUAUUUGAGCGGAGUGUGUUGUAGACCUAUCAGCUGGUAGCUAGGGUAAUGGCCUAGGUAGGCGACGACGGGAGACGGGGGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACUACGUCCAAGGAUGGCAGCAGGCGCGAAACUUGCCUAAUCCUGUGGGGAGGCGGUUAUGAGACGUAUGAUAUUGUUAUGAAGCGGACGAUGAAAGAGUCAGUGGAUAUUGGAGGGCAAGUCGGGUGCCAGCAGCCGCGGUAAUACCUGCUCCGAUGGUGUCUAUGGUGAAUGCUGCGGUUAAAAAGUCUGUAGUCAAGUGAGGAUGUGUAUGAGUAUGAAGGUGAGUGAACUAGAGUUGAAUAAGCUUGUAUGUAUGAGGAGAGCAACGGAGGGGGUGCACUGGAUAGCUGGGCGAGAGGUGAAAUGUGAAGACCCUGGCUGGACGAACGGAGGCGAAGGCUGUGUGCCAUGACGAAUGUGAUGAUCAAGGACGAAGGCCAGAGGAUCGAAAUCGAUUAGAUACCGUUUUAGUUCUGGCAGUAAACGAUGCUGACGGGAUGACAUGUAUGUGUGUUAUGCAAGAGAAAUUGAGUAUGUGAGCUCUGGGGAUAGUAUGUUCGCAAGGGUGAAACUUAAAGAGAUUGACGGAAGGACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCAGGGCUGAAGAUGUGUGGAGAACUGAGAGGGGAGCACAUUGGCGGUGGUGCAUGGCCGUUUGAAACGGAUGGCGUGAGCUGAGGAUUAAUUUCCGGAAGGCGUGAGACCCACAAGACAGGUUGUUUGGAUGACAGGAGGGAGUGGAACAGAACAGGUCCGUUAUGCCCUGAGAUGUCCUGGGCGGCACGCGCACUACGAUACGUGUAUGAGAUGUGUGAGGGAUGAAUGUGUGGAAUGGCAUUCUGAACGUGGAAUUCCUAGUAAUGGUGGCUCAACAAGCCGACGUGAAUGUGUCCCUGUCCUUUGUACACACCGCCCGUCGCUAUCUGAGAUGGCACAUGGGACGAACACCGAGGGGUGUGAGUCUUCUGUGGUAGAUGAGAUAUAAGUCGUAACAUGGCUGCGGUUGGAGAACCAGCUGCAGGAUCAUCA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq new file mode 100644 index 0000000..7ec9865 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.cuniculus.seq @@ -0,0 +1,2 @@ +>d.16.e.O.cuniculus +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGCGCUGACUCCCUUUGUGUGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCUCCCCGCCGGCCGGGGGGGUGGGGCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCAGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUCGCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGUGGAGGGUGCGUAGCGGGCGGUCCGCCGCGAGGCGAGCCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq new file mode 100644 index 0000000..d6a7e62 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.1.seq @@ -0,0 +1,2 @@ +>d.16.e.O.granulifera.1 +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGUGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCUCGUUUGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUUGGUAUUCAUUUACUGGUUUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUCGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUCGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAACCAAUCUCCGAUUGGCUGCGACUUCUUAGAGGGACUUUGUGGGCCAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGCGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAACCUUUUGGACUGCGCGAGGCCCCGAGCCUUGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq new file mode 100644 index 0000000..024562d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.granulifera.2.seq @@ -0,0 +1,2 @@ +>d.16.e.O.granulifera.2 +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAACUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUCUUACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGAUUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCACAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCUGAUGUCCGCAUGUUUGCGUGUGCAGAGCGCCCUCCCAUCCUUCUGUUAACGUUUCUUGGUAUUCAUUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUCGGGGGCAUUAGUACUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCAUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAACCAAUUCCGAUUGGCUCCGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACACAUACAACGAGUACAUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGUGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCAUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCUUACCGAUUUUGAGUGAUCCGGUGAACCUUUUGGACUGCGCGGAGUCUCGUGCUCUGUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq new file mode 100644 index 0000000..f69e872 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.longa.seq @@ -0,0 +1,2 @@ +>d.16.e.O.longa +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUCGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUAAAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCUUUUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAAGGGGUGCCAAUGUCCGCUGUUGCGUGUUCAGCGGCGCCCCUUCAUCCUUCUGUUAACGUCUCGGGUAUUCAUUUACUCGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCUAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGUCCCGUUGCUAAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAACCUUUUGGACUGCGUGGUCCUCGUGGCCGUGCGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq new file mode 100644 index 0000000..4acb186 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.operophterae.seq @@ -0,0 +1,2 @@ +>d.16.e.O.operophterae +CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGCCUCCGAGGCUAAGCCAUGCAUGCCCGUGACGCAAGGAACGGCGAACGGCUCAGUAAUACUGCGAUGAUCUGCUCCGCGCGGACGAUAACUACGGGAAACUGUGGCUAAGAGCGCGGAUUGAGACGCAGCCCUAUCAGCAAGUUGGUAGUGUAACGGACUACCAAGGCGGCGACGGGUGACGGGAAAUCAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUCUCUUGCGAGGAGGCGGUUACGAGGCGUGACGGAAGGGCGCACUGUAAAGACGUGCGCGAACGCGAUUGGAGGGCAAGUUCGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUCUAUGGUGGAUGCUGCAGUUAAAAAGUCCGUAGUCGGCACUGCGACGAAAGCGCGCUGCUCGAUGGCGCAGGCGUUGCAGGGGCUUGCGGAGCGGGCGGGGGGCACGGUAUAGGCAGGCGAGAGAUGAAAUGGCCAAGACCCUGCCUGGACCGACGGUGGCGAAGGCGGUGCCCUCGCACGCAUCUGUGGAUCAAGGACGAAGGCCGGAGGAUCGAAAGUGAUUAGAGACCGCUGUAGUUCCGGCAGUAAACGAUGCCGACACCGCGCGGCGGGGCUGCGCGGGGGGAGAAACCUUAGUGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGUGUGAAAAUUAAACGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGCACCUUACCAGGGCCACGCGCGCCUGAGACCGCAUGCGCGAGGCGCGCAGGAGUGGUGCAUGGUCGUUGCAAAUUGGUGGGGCGACUUUUGGCUUAAAUGCCGGAACGAGUGAGAUCUCCGAGACGGGUGCGCGCAGCACAGGAGGGUGGAGGCGAUAACAGAUCAGUGAUGCCCUUAGAUGCCCUGGGCUGCACGCGCAAUACAAUCCCCGCGCGCUGCACAGAACGGUCGCGGGGGUGUGGGACCGGCGCCUGUAAGGGCGCCGCGAACGAGGAAUUCCUAGUAACGGCGGCUCACCAAGCCGCGGUGAAUGUGUCCCUGUAGCUUGUACACACCGCCCGUCACUAUCUCAGAUGGCCGUGUCGGUGAAGGGAGCAAUCUCUGUGCCUCCGCGGCUAGAUAAGAUGUAAGUCGUAACAAGGUUGCGGUCGGUGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq new file mode 100644 index 0000000..aae8387 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.quadricornutus.seq @@ -0,0 +1,2 @@ +>d.16.e.O.quadricornutus +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGCUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGACGAUUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCUCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCGUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGAGUGCCAAUGUCGUCUUGUUGACUGUGCAGCGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGCUAUUUAUUUAGUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGUCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGAUUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUACCUCCGUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUUGACUCGUUGCUAAGCGAGAUUAACUUCUUAGAGGGACUUUGUGACUARACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGAGGUCCUCGUGACUUUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq new file mode 100644 index 0000000..e0d3525 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.O.sativa.seq @@ -0,0 +1,2 @@ +>d.16.e.O.sativa +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGCAAGUAUGAACUAAUUCGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCCGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCCGCCCGCUGAUCCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCCUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCGCUUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCGCGGCCGGGCCGGUCCGCCUCACGGCAGGCACCGACCUGCUCGACCCUUCUGCCGGCGAUGCGCUCCUGGCCUUAACUGGCCGGGUUCGUGCCUCCGGCGCCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCGGCGGAUGUUGCUUAUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGGGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGCAGCUAGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCACGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGUAUCCAACGAGUAUAUAGCCUGGUCCGACAGGCCCGGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAUCGCGGCGACGGGGGCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq new file mode 100644 index 0000000..0d42d11 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anophelis.seq @@ -0,0 +1,2 @@ +>d.16.e.P.anophelis +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUCGCCUUAAAGACUAAGCCAUGCAAGUUUGCGAGCUGAGCAGCGAACGGCUCAGUAAAACAGGGCACUCUAACGCACGGAAGAGAUAACCACGGGAAACUGUGGCUGAGAAGUGCGAUGAGGCUCUGACCUAUUAGUUUGUCGGUACGGUAAGUGCGUACGGAGACGAUGAUGGGUAACGGGGGAUCAAGUCCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUGCCACGUCCAAGGACGGCAGCAGGCGCGCAACUUACCCAAUGAGGAUUGAGGUAGUGACGAGGCGUAGAUUGUGAGUUGAGAGUAAAGAACUUAACGAGAGCGACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGGGGCGUAUGUGUGUGUUGCUGCGGUUAAAAAGCGCGUAGUUUGUGGUGUAGCGGGUCGUUGUGGGGCGAGAUCAAUGCGUUCUGUGUGACUUAUGCUCAUUGCUAGGGAGCGCGAGACGCCGGUGGUAUUCGGUAGCGAGGGGUGAAAACUGCAGACCUACCGAGGAGCGACAGAGGCGUAAGCGGCCGGCGAGUGCGGAUCCGACGAUCAAGCGCGUGGGCAGGAGUAUCGAAGACGAUUAGAGACCGUCGUAGUUCCUGCAGUAAACGAUGCCGACAUGGUUGAAUAGAAUUGACCAAAGGGAAACUGAGUGUACGGGCUCCGGGGAGAGUACGGGCGCAAGCCAGAAACUUGAAGAAAUUGACGGAAGGACACCACCAGGCGUGGAGUGUGCGGGUUAAUUUGACUCAACGCGGGGCAACUUACCCGGGCCGCAGCCUCUUGAGAGGAAACCGAUGGGGCCUCGUGGUGCAUGGCCGUUCUCAACGCGAGGGGUGACCACUGAGUUAGUUCUGGCAAGCCGUGAGGCCCCUGUACUUUUGUAGACGGCGGACGGCAAGUCCGAGGAAGCGAGGGCGUAUAACAGGUCUGUGAUGCCCGCAGAUGUCCGGGGCUCCACGCGCACUACAAUAGCAAAUGGUAGACGAGAGUAAGUUUGUUGUGGUUGGGAUUGACGCUUGUAAAUGCGUCAUGAACGAGGAAUGCCUAGUAGUUGUCUGUCAGCAGCGGACAACGAAUAAGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCUAAGAUGGCGGUGCGGAUGAAGCUGCUACGUGGCAAGAAUCCGUGCUGCUAGAUUGGAUACAAGUCGUAACAUGGUUGCAGUAGGUGAACCUGCCGCAGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq new file mode 100644 index 0000000..bf550f0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.anserina.seq @@ -0,0 +1,2 @@ +>d.16.e.P.anserina +UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUAUACAGCGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAUUACCUUACUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAUCCCGACUUCGGAAGGGAUGUGUUUAUUAGAUUAAAAACCAAUGCCCUCCGGGGCUCACUGGUGAUUCAUAAUAACCUCUCGAAUCGCACGGCCUUGCGCCGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGACGGCUGGGUCUUGGCCAGCCAUGGUGACAACGGGUAACGGGGAGUUAGGGCUCGACUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUACUGAUACAGGGCUCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGAGGUUAAAAAGCUCGUAGUUGAACCUUGGGCCCGGCCCUCCGGUCCCCCUCACCGGGUGCACUGGCUCGGCCGGGCCUUUCCUUCUGGAGAACCGCAUGCCCUUCACUGGGCGUGCCGGGGAACCAGGACUUUUACUCUGAACAAAUUAGAUCGCUUAAAGAAGGCCUAUGCUCGAAUAGUCUAGCAUGGAAUAAUGGAAUAGGACGUGUGGUUCUAUUUUGUUGGUUUCUAGGACCGCCGUAAUGAUUAAUAGGGACAGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUAAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAGGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGAUUAGGGAUCGGACGGUGUUAUUUUUUGACCCGUUCGGCACCUUGCGAUAAAUCAAAAUGUUUGGGCUCCUGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACGAUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUCGUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUGCUAAAUAGCCCGCAUCGCUUUGGCGGUGCGCCGGCUUCUUAGAGGGACUAUCGGCUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGACAGAGCCAGCGAGUACUCCCUUGGCCGGAAGGCCCGGGUAAUCUUGUUAAACUCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGCUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUCAGUGAGGCUUCCGGACUGGCCCAGGGAGGUCGGCAACGCCAACCCAGGGCCGGAAAGCUAUCCAAACUCGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUCUCCGUUGGUGAACCAGCGGAGGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq new file mode 100644 index 0000000..054fe8f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.carinii.seq @@ -0,0 +1,2 @@ +>d.16.e.P.carinii +UACCUGGUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAGUUAUACAGUGAAACUGCGAAUGGCUCAUUAUAUCAGUUAUAGUUUAUUUGAUAGUAUCUUACUACUUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCAAAAAAUCCCGACUUUAUGGAAGGGAUGUAUUUAUUAGAUAAAAAACCAAUGCCUUCGGGCUUUUUGGUGAUUCAUGAUAACUUCGCGGAUCGCAUGGCCUUGUGCUGGCGAUGAUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGAGGCCUACCAUGGUUUCGACGGGUAACGGGGAAUAAGGGUUCUAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUACAGGGCUCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAGAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGAAUUUAGGGAUUGGUUGCCUGGUCCUCCGAAGUUGUGUGCACUGGCGCAACUGAUCCUUCCCUCCUGGAUUACCGGCUGCCCUUCGCUGGGUGUGCCGGAUAGCCAGGGCAUUUUACUUUGAGAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCUCGAAUACAUUAGCAUGGAAUAAUAAAAUAGGACAUGUGGUUCUAUUUUGUUGGUUUCUAGGACCAUUGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUCAAUUGUCAGAGGUGAAAUUCUUAGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGAGAUCGGGCGAUGUUUUUUUCUUGACUCGCUCGGCAUCUUAUGAGAAAUCAAAGUCUUCGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGAAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUGCUAAAUAGCCAGAUUAGCUUUUGCUGAUCGCGGGCUUCUUAGAGGGACUGUUGGCAUGAAGCCAAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGACAGAGCCAGCAAGUUCAUUUUCCUUGGCCGAAAGGUCUGGGUAAUCUUGUGAAACUCUGUCGUGCUGGGGAUAGAGCAUUGCAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUAUGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAAUGAGGUCUUCGGACUGGUGAUGGGUUAUUGGCAACGAUAAGCCUAUUACUGGAAAGUUGAUCAAAUUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq new file mode 100644 index 0000000..3a8ce15 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.cristatellae.seq @@ -0,0 +1,2 @@ +>d.16.e.P.cristatellae +CACCAGGUUGAUUCUGCCUGACGUAUGCGCUUGUCUUGAAGAUUUAGCCAUGCAAGCUAGCGAAGCCUUAUGGUGGAGCGGCGGACAGCUCAGUAAUACAGUUAUUAUUUACUCGUAGUAUGUAUACGGAUAACCAUGGUAAGCUAUGGCUAAUACGUGAACAGGUUAUUGCAUAGAUGAAACAGCGAUAACUGAGAGAGCAAUCGACUACGACUAAGUUUCUGGCCUAUCAGCUAGAUGGUAAGGUAAUGGCUUACCAUGGCUAUAACGGGUAACGGGAAAUCAGUGUUUGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAACUUACCCAAUUCCUUAGCGGGAGAGGUAGUGAAGAGACAUGAAGUUCUACUUAGAGACUGUACGGUAAAAUAGUACAGGAUCUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGCGCAUAUAAUAGUUGCUGCAGUUAAAACGUCCGUAGUUGAUCACAAGGUAUUCUUCUGCAUAGUAUUUGUGGAGUGUAUCUCGAUACUGUGAGAAAAAUAUGGUUCUCAAAGCGGAUUACGUGAGUAAUUUAGCAUGGGACAUGGUGAAUAUAGGAACAGAUGAUGGCAAUAGUAUUCAGCAGUUAGAGGUGAAAAUCGUUGACCUGCUGAGGACUCUCUGAAGCGAAAGCGAUUGUCAAGUAUGUCUCCGUUAAUAAAGGACUUAAGCUGGAGUAUCGAAGAUGAUUAGAUACCGUCGUAGUUCCAGCUGUAAACUAUGCCGACUAGGUGAGGCCGUCAGGCUGCGCCUUAGGAGAAAUCAAAGUUUUUGGGCUCUGGGGAUAGUAUGGAUGCAAAUCUGAAACUUAAAGAAAUUGACGGAAGGACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGCAACUUACCAGGGCCGAAUGCAUAGGAGAUCGGCUGUCUGAGAGGGUACCCGAGAUUAUGCAGGAGGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGGCCUGUCUGGUUAAUUCCGUAAACGCGUGAGGCCUGGGAAGCAAUUCAUUGCUUGACGGAUAGCGGCAAGCUAUAGGAAGACAGGCUAUAACAGGUCAGUGAUGCCCCUAGAUGUUCUGGGCUGCACGCGCAAUACAAUGGUAUAGUGAGACUAUGUACUGAAAAGUAUGCUUUAAGCUAUAUCGAAUCUGGGAUAAGCUCUUGUAAAUGAGUUUUGAACGAGGAAUUCCUAGUAAUCGCAGGUCAUAAUGCUGCGAUGAAUGCGUCCCUGUUCUUUGUACACACCGCCCGUCACUAUCUUAGAUGGAUGUAUCGGUGAAAUGGCUGGACGAAAGAAAGGCAGUUGAACCUAUACAAUUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGGUGAACCUGUGGCAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq new file mode 100644 index 0000000..66edb7f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.A.seq @@ -0,0 +1,2 @@ +>d.16.e.P.falciparum.A +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUAUAUAUAUAUUUUAUAUGUAGAAACUGCGAACGGCUCAUUAAAACAGUUAUAGUCUACUUGACAUUUUUAUUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCUUUAUUAUCCUUGAUUUUUAUCUUUGGAUAAGUAUUUGUUAGGCCUUAUAAGAAAAAAGUUAUUAACUUAAGGAAUUAUAACAAAGAAGUAACACGUAAUAAAUUUAUUUUAUUUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUGCAAGGCCAAUUUUUGGUUUUGUAAUUGGAAUGGUGGGAAUUUAAAACCUUCCCAGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAAUCGAUAUUUUAUUGUAACUAUUCUAGGGGAACUAUUUUAGCUUUUGGCUUUAAUACGCUUCCUCUAUUAUUAUGUUCUUUAAAUAACAAAGAUUCUUUUUAAAAUCCCCACUUUUGCUUUUGCUUUUUUGGGGAUUUUGUUACUUUGAGUAAAUUAGAGUGUUCAAAGCAAACAGUUAAAGCAUUUACUGUGUUUGAAUACUAUAGCAUGGAAUAACAAAAUUGAACAAGCUAAAAUUUUUUGUUCUUUUUUCUUAUUUUGGCUUAGUUACGAUUAAUAGGAGUAGCUUGGGGACAUUCGUAUUCAGAUGUCAGAGGUGAAAUUCUUAGAUUUUCUGGAGACGAACAACUGCGAAAGCAUUUGUCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUGCCGACUAGGUGUUGGAUGAAAGUGUUAAAAAUAAAAGUCAUCUUUCGAGGUGACUUUUAGAUUGCUUCCUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGCGAGUACACUAUAUUCUUAUUUGAAAUUGAACAUAGGUAACUAUACAUUUAUUCAGUAAUCAAAUUAGGAUAUUUUUAUUAAAAUAUCCUUUUCCCUGUUCUACUAAUAAAUUGUUUUUUACUCUAUUUCUCUCUUCUUUUAAGAAUGUACUUGCUUGAUUGAAAAGCUUCUUAGAGGAACAUUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUAUAUAACGAGUUUUUAAAAAUAUGCUUAUAUUUGUAUCUUUGAUGCUUAUAUUUUGCAUACUUUUCCUCCGCCGAAAGGCGUAGGUAAUCUUUAUCAAUAUAUAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUCAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUGAAUUGUUUGGACAAGAAAAAUUGAAUUAUAUUCUUUUUUUUCUGGAAAAACCGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq new file mode 100644 index 0000000..b5b366a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.falciparum.S.seq @@ -0,0 +1,2 @@ +>d.16.e.P.falciparum.S +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCACAGAUUAAGCCAUGCAAGUGAAAGUACAUAUGUAAGUAAUAUAUUGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGAUGUUUUUAAUAUAAGGAUAACUACGGAAAAUCUGUAGCUAAUACUUGUGAAAAUACCUUUUGAUAUAUACAUAUGUAUGUAUCAUUAAGGUAUGUAUUUGUUAGAUAUAAGAAUAAAAUAAAUAUAAUUGAAUUAUAACAAAGAAGAAACACAUAAAAUAUGUGUAUUAUCAAUCGAGUAUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGACCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAAAAGAGAGGUAGUGACAAGAAAUAACAAUACAAUAUCGAAAAAUGAUUUUGUAAUUGGAAUGAUAGGAAUUUACAAGGUUCCUAGAGAAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAAUUGUUGCAGUUAAAACGUUCGUAGUUGAAUAUUAAAGAAUCCGAUGUUUCAUUUAAACUGGUUUGGGAAAACCAAAUAUAUUAUAUAUUUUGCUUUGUUCAAAAUAAGGUUUUCUAAUAAAUUAUGUUUUUAUCAGAUAUGACAGAAUCUUUUUUAAAAUCUCUUCAAUAUGCUUUUAUUGCUUUUGAGAGGUUUUGUUACUUUGAGUAAAAUUAAGUGUUCAUAACAGACGGGUAGUCAUGAUUGAGUUCAUUGUGUUUGAAUACUACAGCAUGGAAUAACAAAUAUGAAUAAGCUAAUUAUUUUUUUUUUCAUUAUUUUUUUUGAUAUUCUUAUUAGCUUAGUUACGAUUAAUAGGAGUAGCUUUGGGGGCAUUCGUAUUCAGAUGUCAGAGGUGAAAUUCUAAGAUUUUCUGGAGACGGACUACUGCGAAAGCAUUUGCCUAAUCUAUUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUACCGACUAGGUGUUGGAUGAAUAUAAAAAAUAUAUAAAUAUGUAGCAUUUCUUAGGGAAUGUUGAUUUUAUAUUAGAAUUGCUUCCUUCAGUACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGUAAGUACACUAUAUUUUUAUUUGAAAUUGAAUAUAGGUUACUAUACGUUUAUUCAGUGUUCAAAUUAGGAUAUUUUUUUUAUUAAAAUAUUCUUUUCCCUGUUUUACUAAUAAUUUGUUUUUUUUUACUCUAUUUCUCUCUUCUUUUAAGAAUGUACUUGCUUGAUUAAAUAAAGCUUCUUAGAGGAACAGUGUGUAUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUAAACUAGGCUGCACGCGUGCUACAAUGAUAUAUAUAACAAGUUGUUAAAAAUGUACUUAUAAAUAAGUGUGUACAAUUUUUCCUGUACUGAAAAGUAUAGGUAAUCUUUAUCAGUAUAUAUCGUAAUUGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUUAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUAAAUUGUUUGGAUAUGAAUUAAAAUAAUGAAAUUUUAUAUUUCUGAUUUUUUCUAGAAGAACUGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq new file mode 100644 index 0000000..74cb22c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.hippoglossoideos.seq @@ -0,0 +1,2 @@ +>d.16.e.P.hippoglossoideos +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUUUCAUAGGUUAAGCCAUGCAUGUGUAAGCGAAGCUUUUAGUGGAGCGGCGCAAGGCUCAGUAACGGGCGUCUGAUUUGAUCUCUCGGAGUGGACAACCUCUGUAACCGGAGGCCAAAACACGGGAGGGGCAUGCAGUGGAGAUGCCCCGAGAACAUUUAGUGAGAGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAGGACGGGUACGGGGAAUUAGAGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUGCAUUCAGGGCGGUAGUAAGGAAACGUGAAAACGAUGUGCAGGUAAAGAAUGCACUAGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGACUGCGUGACUGGCGUGAAAGACCCUUUUAUUCAUUCAAGGGGGGCGCAGCGCCGGAAAAGCAGGGAAUAAGGAGCGGCCGGGGCACAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGUGCAGGGGCGAUUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGAUGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCAGUUCUUAGACUGCGCCGCGGAAGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGACCGCACGAGUGUGGUACACGAUAGGUCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUUGUGAGACCCCUGCUGGCGAGCCAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCACACGAGUUUAUAGAUAGAAGAAAUGGUGAUCGAGAGGAAAUGAGCUUUGCAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGGUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq new file mode 100644 index 0000000..0825b4a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.lepisma.seq @@ -0,0 +1,2 @@ +>d.16.e.P.lepisma +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAGGUUAUACAAUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUAAAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAGGCUUUGCUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCGAUGUCCGCAUGUUGCGUGUGCAGAGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUUUCGAUUGGGAACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUGCAUACAACGAGUACUUCCCAGCUCCGAAAGGUAGCUGGUAAUCAGCAAUAUGCAUCGUGAUGGGGAUAGAUCCUUGGAAUUAUGGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGGUCCGGUGAAUCAUUUGGACUGCGUGAGGUUUCGUACCUCGUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq new file mode 100644 index 0000000..86c7a36 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.mirandellae.seq @@ -0,0 +1,2 @@ +>d.16.e.P.mirandellae +CACCAGGUUGAUUCUGCCUGGCGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGUAAGCGAAGCAUUUUGUGGAGCGGCAUAAGGCUCAGUAACGGGCGUCUAUUUGAUCUCCUGAUGUGGACAACCUCUGUAACCGGAGGCCAAUACACAUGAGGCACUGUUUCCGUUUGGUGGGGUGUCAAUAGCUAUUUAAUUUUUAUAGCGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAGAUGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCGGUGAGGGCGGUAGUAAGGAGACGUGAAUACGAUGUGCAGGUAAAUAAUGCACUAGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGUGUUCGUAGUCGGGCUGCAUGACUGGCGUGAAAGACCUUCCUUUCAAGGGGGUACAGCGCGGGGAAAGCAGAGAAUAAGGAGCGUUUUGGGGUCAGGUUAUUAAGCGACGAGAGGUGAAAUUUAAUGACUCGCUUAGGAGCAACAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGAGCGAGUUUUAUUCGCUUCGCGGAAGAGAAAUUUAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUCAACUCAACGUGGGACAGCUUACCAGGCCGGACGACCGCACGAGUGUAGUACACGAUAGGUUGAAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCUGUUACGAGUAAUGGUGACAGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCACAGAAAGAGAUUAUUGAGAGAUAAUGGUGAUCGAGAGGGAAUGAGCUUUGUAAGAGGCUCAGGAACGAGGAAUUGCUAGUAAUCGCGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGAUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq new file mode 100644 index 0000000..897f945 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.palmata.seq @@ -0,0 +1,2 @@ +>d.16.e.P.palmata +UGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGGUACCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAACGCGGGGUAACCCGUGGUACCAAUCAGAUAUCAAACCAAUGUGUGGUGAUUCAUGAUUUUUUUUCUGAUCGCACGUUAGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAGCGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUAUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGUGGCCCGUGCUGUGCGCGUAAUGCGUGCGGCGCUGGGGCGCGCUUUUGUGGAGGGCGGCGCGUUGUGGCUUCACUGUCGCGGCGUGUCGGCGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGCCGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGCUGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGAUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCAGGCAUUACGAUGACCUGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCCGCUACCAUUGUGUAGCUGUUCGCCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUGAGGAUGCGCGAAAGCGUUUCCCAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGACUGCCGCGGUUGAGGCGUUUACGCCCUGGCCGCAGUGGGAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGACAGAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq new file mode 100644 index 0000000..a076ef4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.pulvinata.seq @@ -0,0 +1,2 @@ +>d.16.e.P.pulvinata +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUGAGUGAUUUAUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGUUACACUACCGGAUAACCGUAGUAAAUCUAGAGCUAAUACGUGCCACUAAAACGGUGAAAACCGUGGUAUAAAUUGGAGAUACAAACCAAUGUUUGGUGAUUCACAAUUUCUUUUCUGAUUGCAAUCAUGUUUUGCGACACAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUAUCAUGGUCGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAGCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAUCUUAUCGAGUAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAAUUUGGCGGGCGAUGUGGGGCGUCUUAACCGACGAUCUCAUGUCGGCUGCCUUUGUGGAGGGGGGCCUAGUGGUGCUUCACUGCAUUGUUAGGUUUCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCGGGCGUUUGCCAUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUCCUGUUUUGUUGGUUUGUGAGGAUCGGGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGGCGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGUGAGACUGUUUUUGGCUCACCCGGCAUCCUUCGGGAAACCAAAGUAUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAGCUAGGCGCUACUACCACUAUGGUAGUAAGGCUUGCCUUCCUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGAUCAACGGGUGAGGAUGUGCGAGAGCAUUUCCCAAUCUCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCACGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAGAUGAACUGUGCUACACAGAUUUUUUGGCCCGAACUUGGUCAAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq new file mode 100644 index 0000000..76544cb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.A.seq @@ -0,0 +1,2 @@ +>d.16.e.P.vivax.A +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUAUAUGCAUAUUUUAUAUGUAGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGACAUUUUUUCUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCCUUAGCACUCUUGAUUCAUUUCUUGAGUGUGUACUUGUUAAGCCUUUUAAGAAAAAAGUUAUUAACUUAAGGAAUUAUAACAAAGAAGCGACACGUAAUGGAUCCGUCCAUUUUUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUGGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUACAAGGCCAAUCUGGCUUUGUAAUUGGAAUGAUGGGAAUUUAAAACCUUCCCAAAACUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAAUCGAUAUUUUAAGCAACGCUUCUAGCUUAAUCCACAUAACUGAUACUUCGUAUCGACUUUGUGCGCAUUUUGCUAUUAUGUGUUCUUUUAAUUAAAAUGAUUCUUUUUAAGGACUUUCUUUGCUUCGGCUUGGAAGUCCUUGUUACUUUGAGUAAAUUAGAGUGUUCAAAGCAAACAGAUAUAGCAUUGCGCGUUUGAAUACUACAGCAUGGAAUAACAAAUUGAACAAGUCAGAAUUUUUGUUCUUUUUUCUUAUUUUGGCUUAGUUACGAUUAAUAGGAGUAGCUUGGGGGCAUUUGUAUUCAGAUGUCAGAGGUGAAAUUCUUAGAUUUUCUGGAGACAAACAACUGCGAAAGCAUUUGCCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUGCCGACUAGGCUUUGGAUGAAAGAUUUUAAAAUAAGAAUUUUCUCUUCGGAGUUUAUUCUUAGAUUGCUUCCUUCAGUGCCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUAAUAGCUCUUUCUUGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGCAAAUACGACAUAUUCUUACGUGGGACUGAAUUCGGUUGAUUUGCUUACUUUGAAGAAAAUAUUGGGAUACGUAACAGUUUCCCUUUCCCUUUUCUACUUAGUUCGCUUUUCAUACUGUUUCUUUUUCGCGUAAGAAUGUAUUUGCUUGAUUGUAAAGCUUCUUAGAGGAACGAUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUGUAUAACGAGUUAUUAAAAUUACGAUUCAGCUUGCUGUUUCGUAUUUUUCCUCCACUGAAAAGUGUAGGUAAUCUUUAUCAGUACAUAUCGUGAUGGGGAUAGAUUGUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCAUGAUUCAUCAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAAGAUAUGAUGAAUUGUUUGGACAAGAAGAAGGGGGAUUAUAUCUCCUUUUUUCUGGAAAAACCGUAAAUCCUAUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq new file mode 100644 index 0000000..13a90ad --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.vivax.S.seq @@ -0,0 +1,2 @@ +>d.16.e.P.vivax.S +AACCUGGUUGAUCUUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAAGUGAAAGUACAUGCAUAUUUUUAUAUGCGGAAACUGCGAACGGCUCAUUAAAACAGUUAUAAUCUACUUGACAUUUUUUUCUAUAAGGAUAACUACGGAAAAGCUGUAGCUAAUACUUGCUUUAAUGCUCUCGACGAAUGUCUUGGGCAUGUACUUGUUAAGCCUUUAUAAGAAAAAAGUUAAUAACUUAAGGAAUGAUAACAAAGAAGUGACACAUAGAAGGACCUGCGUCCAUUUAUAGUGUGUAUCAAUCGAGUUUCUGACCUAUCAGCUUUUGAUGUUAGGGUAUUGGCCUAACAUUGCUAUGACGGGUAACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUUCUAAAGAAGAGAGGUAGUGACAAGAAAUAACAAUACAAGACCAAAACUGGUUUUGUAAUUGGAAUGAUGGGAAUUUAAAUCCUUCCCAUAAUACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAAUUGUUGCAGUUAAAACGCUCGUAGUUGAAUUUCAAAGAACCAAUAUUUUAAUAACGCCGUUAGCUAGAUCCACAAGGGGUUGAGCCAAUCACGGUUUCGGCUUCUGUGCGCAUCCUACCUAUCAAGCGUUUUUUUAAUUAAAGUGUUUCUUUUUAAAAUCUUCUUUACCUUAACCAUAUGGAAGAUUUUGUUACUUUGAGUAAAUUAAAGUGUUCAUAGCAAACAGAUACAGCAUUGCGCGUUUUGAAUACUACAGCAUGGAAUAACAAAAUUGAACAAGUCAAAACUAUGUUUCUUUUUUUUUAUUUUUGGCUUAGUUACGAUUAAUAGGAGUAGUUUGGGGACAUUUGUAUUCAGAUGUCAGAGGUGAAAUUCUAAGAUUUUCUGGAGACAAACAACUGCGAAGGCAUUUGUCUAAAAUACUUCCAUUAAUCAAGAACGAAAGUUAAGGGAGUGAAGACGAUCAGAUACCGUCGUAAUCUUAACCAUAAACUAUACCGACUAGGUUUUGGAUGAAAGUUAAACAAAUAAGGAUAGUCUCUUCGGGGAUAGUCCUUAGAUUUCUUCCUUCAGUACCCUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGCGAGUAUUCGCGCAAGCGAGAAAGUUAAAAGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCUUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACUAGUUUAAGACAAGAGUAGGAUUGACAGAUUGAGAGCUCUUUCUCGAUUUCUUGGAUGGUGAUGCAUGGCCGUUUUUAGUUCGUGAAUAUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGAUCUUAACCUGCUAAUUAGCGGUAAGUACGACAUAUUUUUAUGUCGGAUUGGAUCUGGAUGAUUUGCUUAUAUUGAGGUGCAAUCUAAAUAGGGGAUUGCAAUUAUACUUCGUGUCGGUGUUUCUUAAUCGAAUAGCUGAUGCGUUUGGUAUAUUGCUUUCCUUUUUUUUAUUUCUGCGCUUCUUUACUUGGCUUAUCGUACCGUUUCCUUUUUGUGUAGAAAUGUAUUUGCAUUAUAUUAAAGCUUCUUAGAGGAACGAUGUGUGUCUAACACAAGGAAGUUUAAGGCAACAACAGGUCUGUGAUGUCCUUAGAUGAACUAGGCUGCACGCGUGCUACACUGAUAUGUACAACGAGUUAUUAAAAUUACGAUUCAGCUUGCUGUUACGUAUUUUUCCUCCACUGAAAAGUGUAGGUAAUCUUUAUCAGUACAUAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUGAACGAGGAAUGCCUAGUAAGCACGAUUCAUUAGAUUGUGCUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUCGAAAGAUAUGAUGAAUUGUUUGGACAAGAAGAAAGGGGAUUAUAUCUUCUUUUUUCUGGAAAAACCGUAAAUCCUGUCUUUUAAAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq new file mode 100644 index 0000000..64ca28d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.P.weissei.seq @@ -0,0 +1,2 @@ +>d.16.e.P.weissei +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGAGGGCGCCAAUGUCCGCUGAUUGCGUGUGCAGCGGUGCCCUCUCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUAGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGACCCGUUGCUAAGCGGGCACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACGUCCCAGCUCCGUAAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACCGCGAAGUCCUCGUGGCUUUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq new file mode 100644 index 0000000..7479150 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Ple.lanceolata.seq @@ -0,0 +1,2 @@ +>d.16.e.Ple.lanceolata +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGAUGAUUCAUAAUAACUGAUCGAAUCGCUUCGGCUUUGCCAGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGAGUGCCAAUGUCGUCUUGUUGACUGUGCAGCGGCGCUCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUCGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCAACCCGUUGCUAAGCGGGAAUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGAGGUCCUCGUGAUCUUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq new file mode 100644 index 0000000..093c07a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.carriebowensis.seq @@ -0,0 +1,2 @@ +>d.16.e.R.carriebowensis +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUCUAAGUAUAAGUGAUUCUGAUGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAAUUUCUUCGAUGGUAACUUACUAUUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAAUGCGGGGUUUCGGCUCCGUGGUGCCAAUUAGAUAACAACACCAACAUUUGGUGAUUCAUAAUUUUCUUUCUGAUCGCUGCAUGCAUUGCGGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAGUGUCUUACCAUGGUGGUGACGGGUAACGGACCGUGGGUGCGGGACUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACUCCGGGAGGUAGUGACAAGAAAUAUCAAUAGGGGACCCGAUGGGUGCCCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAAGUUGGUGGUCUUGCGGGUGCGCGCGUUGAGCGUACGCCUGUCGAGGCUGCUUUUGUGGAUUGCGCGCACGGGCGGCUUUAGUGUCGAACGUGUUGGGUUUCGCUGCUUUGGCGUUCACGCGGCAGAGCGGCGGAGGCGCAGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUCGGUUUUCCUAUUUUGUUGGUGUUGUGAGGGGCGAGUAAUGAUUAAGAGGGACAGUUGGGGGCACUUGUAUUCCGGCGCUAGAGGUGAAAUUCUUAGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGAUGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGGGAUCGGGCGUGGAAUUGCGAUGACCCGCCCGGCACCCUCCGGGAAACCAAAGUUUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCAGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAAAUAGGGGCUAUUACCGCUUUUUUUGGUAGUGAGAGCUUUUUUGACCCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGAUCAGCGGGCGAGGAUGCGCGAAAGCGUUUCCUAAUCCCCAAAUCCGCUCGUGCUGGGGAUAGAGGGUUGCAAUUCUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAUCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAUUGUCGUGAGGGGAGCGUUUGCGCUCGUUUCGUGAAGAAAACUUGGUCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq new file mode 100644 index 0000000..99deaaf --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.leptophylla.seq @@ -0,0 +1,2 @@ +>d.16.e.R.leptophylla +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUGAGUGAAUUGUACAACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGAUAUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCACAAGACGACUCAAGUCGUGGUAUAAAUUGGAGAUACAAACCAAUAUUUGGUGAUUCACAAUUUCUUUUCUGAUUGCACUUUCGUGCGACGCAUCGUUCAAAUUUCUGACCUAUCAACUUUGGAUGGUAAGGUAUUGUCUUACCAUGGUUUUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCGGACACCGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCCCGAUGGGUUUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAGCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAACUUGGCGGGCGACUUGCCUCGUCCUCGCGGAUGUUGGCAGGUCGGCCGCCUUUGUGGAGGGGGGCCUAGUGGUUCUUUACUGCAUCGCUAGGUCGCUGCCACCGUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGCCGUGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACCUGUUUUCUAUUUUGUUGGUUUGUUAGAAUCGGGUAAUGAUUAAGAGGGAUGGUUGGGGGCAUUUGUAUUCCAGCGUCAGAGGUGAAAUUCUUGGAUUGUUGGAAGACAAACAGCUGCGAAAGCGUCUGCCAAGGACAUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGGACUGGAGAUCGGGCGGGGCUGUCAUUUGGCCCGCCCGGCAUCCUUCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGGAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUCUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGUUAGCUAGGCGCCAUUACCGCUUUUGGUAGUGAGGCUAGCCUUCCUAAACGGACUGCGGGCGUCUAGCCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGUGCUACACUGAGCGGGUCAACGGGCGAGGAUGUGCGAGAGCAUUUCCAAAUCUCUAAAUCCGCUCGUGCUGGGGAUCGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCACGGGUCAUCAUCCCGUGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGGUCCGGUGAGGCCUUGGGAGGGCUAAAUGGACUGUGUUCUCACGGACCGUUUGGCCCAAACUUGGCCAAGCCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq new file mode 100644 index 0000000..8a1603d --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.R.norvegicus.seq @@ -0,0 +1,2 @@ +>d.16.e.R.norvegicus +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGGUCGCUCGCUCCUCUCCUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGGGCGCUGACCCCCCUUCCCGUGGGGGGGACGCGUGCAUUUAUCAGAUCAAAACCAACCCGGUCAGCCCCCUCCCGGCUCCGGCCGGGGGUCGGGCGCCGGCGGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGCCCUCCGUGGCGGCGACGACCCAUUCGAACGUCUGCCCUAUCAACUUUCGAUGGUAGUCGCCGUGCCUACCAUGGUGACCACGGGUGACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACCCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUCCACUUUAAAUCCUUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAGCGGGCGGGCGGUCCGCCGCGAGGCGAGUCACCGCCCGUCCCCGCCCCUUGCCUCUCGGCGCCCCCUCGAUGCUCUUAGCUGAGUGUCCCGCGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCCGAGCCGCCUGGAUACCGCAGCUAGGAAUAAUGGAAUAGGACCGCGGUUCUAUUUUGUUGGUUUUCGGAACUGAGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGCGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGGACCAGAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUGGCGAUGCGGCGGCGUUAUUCCCAUGACCCGCCGGGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGACAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCCGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCUGGCAUGCUAACUAGUUACGCGACCCCCGAGCGGUCGGCGUCCCCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACCCGAGAUUGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGACUGGCUCAGCGUGUGCCUACCCUACGCCGGCAGGCGCGGGUAACCCGUUGAACCCCAUUCGUGAUGGGGAUCGGGGAUUGCAAUUAUUCCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGCCCUCGGAUCGGCCCCGCCGGGGUCGGCCCACGGCCCUGGCGGAGCGCUGAGAAGACGGUCGAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq new file mode 100644 index 0000000..b728e04 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.alba.seq @@ -0,0 +1,2 @@ +>d.16.e.S.alba +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACGAAUUCAGACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUAACUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGUGCUGCUCUGAUGAUUCAUGAUAACUCGACGGAUCGCAUGGCCUUUGUGCUGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUAACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCAUUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACCUUGGGAUGGGUCGCCCGGUCCGCGUUUGGUGAGCACCGGUCGGCUUGUCCCUUCUGUCGGCGAUACGCUCCUGGCCUUAAUUGGCCGGGUCGUGCCUCCGGCGCUGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUCAUAGGAUUUCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGGACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGAUGUUGCUUUUAGGACUCCGCUGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAAGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUACGUGGAGGCAUCCCUUCACGGCCGGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCGCACGCGCGCUACACUGAUGUAUUCAACGAGUUCACACCUUGGUCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAGUACUCGGAUCGCGGCGACGUGGGUGGUUCGCCGUCCGCGACGUCGCGAGAAGUUUUCUAAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq new file mode 100644 index 0000000..7eb6818 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.cerevisiae.seq @@ -0,0 +1,2 @@ +>d.16.e.S.cerevisiae +UAUCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCAAUUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUCGUUUAUUUGAUAGUUCCUUUACUACAUGGUAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCUUAAAAUCUCGACCCUUUGGAAGAGAUGUAUUUAUUAGAUAAAAAAUCAAUGUCUUCGGACUCUUUGAUGAUUCAUAAUAACUUUUCGAAUCGCAUGGCCUUGUGCUGGCGAUGGUUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUUUCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAUAAAUAACGAUACAGGGCCCAUUCGGGUCUUGUAAUUGGAAUGAGUACAAUGUAAAUACCUUAACGAGGAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUUGGGCCCGGUUGGCCGGUCCGAUUUUUUCGUGUACUGGAUUUCCAACGGGGCCUUUCCUUCUGGCUAACCUUGAGUCCUUGUGGCUCUUGGCGAACCAGGACUUUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUAUUGCUCGAAUAUAUUAGCAUGGAAUAAUAGAAUAGGACGUUUGGUUCUAUUUUGUUGGUUUCUAGGACCAUCGUAAUGAUUAAUAGGGACGGUCGGGGGCAUCAGUAUUCAAUUGUCAGAGGUGAAAUUCUUGGAUUUAUUGAAGACUAACUACUGCGAAAGCAUUUGCCAAGGACGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCGAAGAUGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGGUGGUGUUUUUUUAAUGACCCACUCGGCACCUUACGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACACAAUAAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUUUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGCUUAAUUGCGAUAACGAACGAGACCUUAACCUACUAAAUAGUGGUGCUAGCAUUUGCUGGUUAUCCACUUCUUAGAGGGACUAUCGGUUUCAAGCCGAUGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGACGUUCUGGGCCGCACGCGCGCUACACUGACGGAGCCAGCGAGUCUAACCUUGGCCGAGAGGUCUUGGUAAUCUUGUGAAACUCCGUCGUGCUGGGGAUAGAGCAUUGUAAUUAUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUAGUACCGAUUGAAUGGCUUAGUGAGGCCUCAGGAUCUGCUUAGAGAAGGGGGCAACUCCAUCUCAGAGCGGAGAAUUUGGACAAACUUGGUCAUUUAGAGGAACUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq new file mode 100644 index 0000000..3697105 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lemnae.seq @@ -0,0 +1,2 @@ +>d.16.e.S.lemnae +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCCGACUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAAUCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCAUUUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGAGGGGCGCCAAUGUCCGAUGUUUCGUGUGCAGCGGUGCCUCUCCAUCCUUCAGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCUGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGUUAAGCGGACUUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCAUUUGGACUGCGCGGUCCUCGUGACUGUGUGGAAAAUCUAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq new file mode 100644 index 0000000..2908cfd --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.lophii.seq @@ -0,0 +1,2 @@ +>d.16.e.S.lophii +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGAUUUAGCCAUGCAUGUGUAAGCGAAGCGAUUAGUGAAGCGGCGGAAGGCUCAGUAACGGGCGAGUAUUUUAAUCUCUAGAACCGGACAACCUCAGGAAACAGAGGGGAAAACGGAGUAAGAGCAUGUGUUGUUAGCAUGUGAUGAGAACAACAGUGCAGGAGAGUAAGAAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUAUUUAGACGUAGACGGGUACGGGGGAUUAGGGUUUGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGAAAAUUACCGAAGCCUCCAAGAGGGCGGUAGUGAAGAGACGUGAAAACAAGUGUGUGUAAAAACCACAUGAGUAACUGUGGAGGGUCAAGGCUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCAGGAGUGUCUAUGAUGAUUGCUGCGAUUAAAAGGUCCGUAGUCGAAGAACAGUACUUGUUUGUAAUGUGGCUUAUCGAGAGCCGAAUAGAACGAGAAGAGUUCAGAGUAAGGAGYGAAGGAGGGCUAGAUUAUUGAGCAGCGAGAGGUGAAAUUUGAUGACCUGCUUUAGGAGUAACAGAGGCGAAAGCGCUAGUCAAGAACGAAUCCGAUGAUCAAGGACGUAGGCUGGAGGAUCGAAGACGAUUAGAGAGACCGUAGUAGUUCCAGCAGUAAACGAUGCCUACGCUGUUGUGGUUAUGAGCACGGCAGAAGAGAAAUCUAGUAGGGCUUUGGGGAGAGUACGCGCGCAAGCGAUAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAUACCCGAUGGCCGUGUGAGCGUAGUACGCGAUAGGUCAGAGAGUGGUGCAUGGCCGUUAACGACGAGUGGGGUGACCUUUGGGUUAAGUCCGCCGAAGUAGUGAGAUCCCUAGGAUACGAAAGUUAUCGACAGGUGUUAAAAACACAGGAAGGAAGGGGCAAGAACAGGGUCAGUGAUGCCCUUAGAUGGUAUGGGCUGCACGCGCACUACAGUGGUCACAGCAGAAACGGAUAGAAGUAAAUGUGAUCGAGAGGGAAUGAGCACUGUAAUGUGCACAGGAACGAGGAAUUGCUAGUAAUCGUUAUCUCAUUAAGAAGCGAUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAACCAGGUGCGAACAAGUGAAAGCGAGUGAGUGCAGGGUUCYAGAUCUGAUACAAGUCGUAACAAGGCAGCUGUAGGAGAACCAUUAGCAGGAAGCUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq new file mode 100644 index 0000000..022bce8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.mytilus.seq @@ -0,0 +1,2 @@ +>d.16.e.S.mytilus +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGUUAAGCCCAACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGAUGACUCAUAAUAACUGAUCGAAUCGCAUGGGCUUUGCCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGAGGGGUGCCAAUGUCCGAUUGUUUCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGAUAUUCAUUUAUUGGUCUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGCCUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCGAUCCGUUGUUAAGCGGACUUGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGUUCCGGUGAACCAUUUGGACCACGCGGUCUUCGUGACUGUGAGGAAAAUCUAGUAAACCAUAACACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq new file mode 100644 index 0000000..3e571a9 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.S.tuberosum.seq @@ -0,0 +1,2 @@ +>d.16.e.S.tuberosum +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGUAAGUAUGAACAAAUUCAGACUGUGAAACUGCGAAUGGCUCAUAAAUCAGUUAUAGUUUGUUUGAUGGUAUCUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCUGGAAGGGAUGCAUUUAUUAGAUAAAAGGUCGACGCGGGCUCUGCCCGUUGCUGCGAUGAUUCAUGAUAACUCGACGGAUCGCACGGCCAUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGUGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCUCUAUGAGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACUUUGGGAUGGCACGGCCGGUCCGCCCUAGGUGUGCACCGGUCGUCUUGUCCCUUCUGUCGGCGAUGCGCUCCUGGCCUUAAUGUGCCGGGUCGUGCCUCCGGCGCUGUUACUUGAAGAAAUUUAGAGUGCUCAAAGCAAGCCUACGCUCUGUAUACAUUAGCAUGGGAUAACAUUAUAGGAUUCGGUCCUAUUUACGUUGGCCUUCGGGAUCGGAGUAAUGAUUAACAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACCGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGGUCGGCGGAUGUUGCUUUUAGGACUCCGCCGGCACCUUAUGAGAAAUCAAAGUUUUUGGGUUCCGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGUAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGAAGGUAUCCCUUCGCGGCCAGCUUCUUAGAGGGACUACGGCCUUUUAGGCCGCGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUUCAACGAGCUUAUAGCCUUGGCCGACAGGCCCGGGUAAUCUUUGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUUCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGAUCCGGUGAAAUGUUCGGAUCGCGGCGACGUGGGCGGUUCGCUGCCCGCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq new file mode 100644 index 0000000..9a3b981 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.cruzi.seq @@ -0,0 +1,2 @@ +>d.16.e.T.cruzi +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUUUCAAGGACUUAGCCAUGCAUGCCUCAGAAUCACUGCAUUGCAGGAAUCUGCGCAUGGCUCAUUACAUCAGACGUAAUCUGCCGCAAAAAUCUUGCGGUCUCCGCAAAAUUGGAUAACUUGGCGAAACGCCAAGCUAAUACAUGAACCAACCGGAUGUUCUCUGUUCCGGCGGCAGGGCAACCUGCUGCCAUGGGACGUCCAGCGAAUGAAUGAAAGUAAAACCAAUGCCUUCACCGGGCAGUAACACUCAGAAGUGUUGAUUCAAUUCAUUCCGUGCGAAAGCCGGGUUUUUUAUCCGGCGUCUUUUGACGAACAACUGCCCUAUCAGCCAGCGAUGGCCGUGUAGUGGACUGCCAUGGCGUUGACGGGAGCGGGGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAAUAGCUACCACUUCUACGGAGGGCAGCAGGCGCGCAAAUUGCCCAAUGUCAAAAAAAAAAGAUGAGGCAGCGAAAAGAAAUAGAGCCGACAGUGCUUUUGCAUUGUCGUUUUCAAUGGGGGAUAUUUAAACCCAUCCAAAAUCGAGUAACAAUUGGAGGACAAGUCUGGUGCCAGCACCCGCGGUAAUUCCAGCUCCAAAAGCGUAUAUUAAUGCUGUUGCUGUUAAAGGGUUCGUAGUUGAAUUGAGGGCCUCUAAGGCGCAAUGGUUUAGUCCCAUCCACUUCGGAUUGGUGACCCAUGCCCUUGUGGUCCGUGAACAGACAUAUUCAGAAACAAAAAACACGGGAGUGGUACCUUUUCUGAUUAUCGCAUGUCAUGCAUGCCAGAGGGCGCCCGUGAUUUUUUACUGUGACUAAAAAAGUGUGACCAAAGCAGUCAUUCGACUUGAAUUAGAAAGCAUGGGAUAACAAAGGAGCAGCCUCUGGGCCACCGUUUCGGCUUUUGUUGGUUUUAAAAGUCCAUUGGAGAUUAUGGGGCAGUGUGACAAGCGGCUGGGUGGUUAUUCCACACACACGCACACUCCUUUUUUGGAUGUUGUGUCUCUGUGUGUGUGGCACUCGUCGCCUUUGUGGGAAAUCCGUGUGGCACUUGUUUGGUGUUGUUGGCAGACUUCGGUCUUGCCUUCACACACGUUUCACAUGUGUCAUGCCUUCCCUCAACUCACGGCAUCCAGGAAUGAAGGAGGGUAGUUCGGGGGAGAACGUACUGGUGCGUCAGAGGUGAAAUUCUUAGACCGCACCAAGACGAACUACAGCGAAGGCAUUCUUCAAGGAUACCUUCCUCAAUCAAGAACCAAAGUGUGGGGAUCGAAGAUGAUUAGAGACCAUUGUAGUCCACACUGCAAACGAUGACACCCAUGAAUUGGGGAGUUUUUGGUCGUAGGCGUGGUCGGGCUUGAUUAUAUUAUUUUUCAUCCCGUUCCUCGUCUCGCCAAUGAAUAUAUUAAAUUUACGUGCAUAUUCUUUUUGGUCUUCGUUUUUUUACGGCGAGGACCUUUAACGGGAAUAUCCUCAGCACGUUAUCUGACUUCUUCACGCGAAAGCUUUGAGGUUACAGUCUCAGGGGGGAGUACGUUCGCAAGAGUGAAACUUAAAGAAAUUGACGGAAUGGCACCACAAGACGUGGAGCGUGCGGUUUAAUUUGACUCAACACGGGGAACUUUACCAGAUCCGGACAGGGUGAGGAUUGACAGAUUGAGUGUUCUUUCUCGAUCCCCUGAAUGGUGGUGCAUGGCCGCUUUUGGUCGGUGGAGUGAUUUGUUUGGUUGAUUCCGUCAACGGACGAGAUCCAAGCUGCCCAGUAGGAUUCAGAAUUGCCCAUAGGAUAGCAAUCCCUUCCGCGGGUUUUACCCAAGGGGGGGCGGUAUUCGCUUGUAUCCUUCUCUGCGGGAUUCCUUGUUUUGCGCAAGGUGAGAUUUUGGGCAACAGCAGGUCUGUGAUGCUCCUCAAUGUUCUGGGCGACACGCGCACUACAAUGUCAGUGAGAACAAGAAAAACGACUCUUGUCGGACCUACUUGAUCAAAAGAGUGGGAAAACCCCGGAAUCACGUAGACCCACUUGGGACCGAGUAUUGCAAUUAUUGGUCGCGCAACGAGGAAUGUCUCGUAGGCGCAGCUCAUCAAACUGUGCCGAUUACGUCCCUGCCAUUUGUACACACCGCCCGUCGUUGUUUCCGAUGAUGGUGCAAUACAGGUGAUCGGACAGUCGAGUGCUUCACUUGACCGAAAGUUCACCGAUAUUUCUUCAAUAGAGGAAGCAAAAGUCGUAACAAGGUAGCUGUAGGUGAACCUGCAGAAGGAUCAAGCUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq new file mode 100644 index 0000000..c3f9ae2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.gondii.seq @@ -0,0 +1,2 @@ +>d.16.e.T.gondii +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUUAAAGAUUAAGCCAUGCAUGUCUAAGUAUAAGCUUUUAUACGGCUAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUGGUCUUUACUACAUGGAUAACCGUGGUAAUUCUAUGGCUAAUACAUGCGCACAUGCCUCUUCCCCUGGAAGGCAGUGUUUAUUAGAUACAGAACCAACCCACCUUCCGGUGGUCCUCAGGUGAUUCAUAGUAACCGAACGGAUCGCGUUGACUUCGGUCUGCGACGGAUCAUUCAAGUUUCUGACCUAUCAGCUUUCGACGGUACUGUAUUGGACUACCGUGGCAGUGACGGGUAACGGGGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGAUUCAGGGAGGUAGUGACAAGAAAUAACAACACUGGAAAUUUCAUUUCUAGUGAUUGGAAUGAUAGGAAUCCAAACCCCUUUCAGAGUAACAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGCUGGAAGCAGCCAGUCCGCCCUCAGGGGUGUGCACUUGGUGAAUUCUAGCAUCCUUCUGGAUUUCUCCACACUUCAUUGUGUGGAGUUUUUUCCAGGACUUUUACUUUGAGAAAAUUAGAGUGUUUCAAGCAGGCUUGUCGCCUUGAAUACUGCAGCAUGGAAUAAUAAGAUAGGAUUUCGGCCCUAUUUUGUUGGUUUCUAGGACUGAAGUAAUGAUUAAUAGGGACGGUUGGGGGCAUUCGUAUUUAACUGUCAGAGGUGAAAUUCUUAGAUUUGUUAAAGACGAACUACUGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGCUCGAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGAGAUAGGAAAACGUCAUGCUUGACUUCUCCUGCACCUUAUGAGAAACCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACCAGGUCCAGACAUAGGAAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAAAUAGGAUCAGGAACUUCGUGUUCUUGUAUCACUUCUUAGAGGGACUUUGCGUGUCUAACGCAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCUGCACGCGCGCUACACUGAUGCAUCCAACGAGUUUAUAACCUUGGCCGAUAGGUCUAGGUAAUCUUGUGAGUAUGCAUCGUGAUGGGGAUAGAUUAUUGCAAUUAUUAAUCUUCAACGAGGAAUGCCUAGUAGGCGCAAGUCAGCACGUUGCGCCGAUUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGUUCCGGUGAAUUAUUCGGACCGUUUUGUGGCGCGUUCGUGCCCGAAAUGGGAAGUUUUGUGAACCUUAACACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq new file mode 100644 index 0000000..22f2555 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.hominis.seq @@ -0,0 +1,2 @@ +>d.16.e.T.hominis +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGCAAGCGAAGCCGGUGGUGGGGCGGCGCAAGGCUCAGUAACGGGCGACUGAUUUGAUCUCCCGGUGUGGACAACCUCUGUAAACGGAGGCCAAAACACAGGAGCGCCGUGUACAGAGACGGUGCGAGAACCGGAGGUGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGCAAAUUACCGAAGCCCGCGUUCGGGGCGGUAGUAAGGAGACGUGUAAGCGAUGUGCAGGUAAAAUAUGCACUGGUAACAGGAGGUAAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGAUGAUUGCUGCAGUUAAAGAGUUCGUAGUCGGGCUGCGUGACUGGGGUUUAAGGCCCGCUAUCGAGGCGGGCAGUGCGCCAGAAAAGCAGAGGAUGAGGAGCGGCCGGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAGCAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCGGUGAGCCGCCACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGAGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGGACAGCUUACCAGGCCCGACGGUCGCAUGAGUGUUGUACACGAUAGGCCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCCGGCGUGCCGGGACAGGUGCGCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAUGGCAGAGGUAGCCUGAAUGGCGAUCGAGAGGGAACGAGCUCUGGAAGGGGCUCGGGAACGAGGAAUUGCUAGUAAUCGUGGGCUCAUUAAGACGCGAUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq new file mode 100644 index 0000000..15995cb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.thermophila.seq @@ -0,0 +1,2 @@ +>d.16.e.T.thermophila +AACCUGGUUGAUCCUGCCAGUUACAUAUGCUUGUCUUAAAUAUUAACCCAUGCAUGUGCCAGUUCAGUAUUGAACAGCGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUUAAAGAUUACAUGGAUAACCGAGCUAAUUGUUGGGCUAAUACAUGCUUAAAAUUCCGUGUCCUGCGACCGGAACGUAUUUAUUAGAUAUUAGACCAAUCGCAGCAAUGUGAUUGAGAUGAAUCAAAGUAACUGAUCGGAUCGAGGUUUACCUCGAUAAAUCAUCUAAGUUUCUGCCCUAUCAGCUCUCGAUGGUAGUGUAUUGGACUACCAUGGCAGUCACGGGUAACGGAGAAUUAGGGUUCGAUUCCGGAGAAGGAGCCUGAGAAACGGCUACUACAACUACGGUUCGGCAGCAGGGAAGAAAAUUGGCCAAUCCUAAUUCAGGGAGCCAGUGACAAGAAAUAGCAAGCUGGGAAACUUACGUUUCUACGGCAUUGAAAUGAGAACAGUGUAAAUCUCUUAGCGAGGAACAAUUGGAGGGCAAGUCAUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAACUUCUGUUCAGGUUCAUUUCGAUUCGUCGUGUGAAACUGGACAUACGUUUGCAAACUAAAAUCGGCCUUCACUGGUUCGACUUAGGGAGUAAACAUUUUACUGUGAAAAAAUUAGAGUGUUCCAGGCAGGUUUUAGCCCGAAUACAUUAGCAUGGAAUAAUGGAAUAGGACUAAGUCCAUUUUAUUGGUUCUUGGAUUUGGUAAUGAUUAAUAGGGACAGUUGGGGGCAUUAGUAUUUAAUAGUCAGAGGUGAAAUUCUUGGAUUUAUUAAGGACUAACUAAUGCGAAAGCAUUUGCCAAAGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACUAUAAACUAUACCGACUCGGGAUCGGCUGGAAUAAAUGUCCAGUCGGCACCGUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGAAGUAUGGUACGCAAGUCUGAAACUUAAAGGAAUUGACGGAACAGCACACCAGAAGUGGAACCUGCGGCUUAAUUUGACUCAACACGGGGAAACUCACGAGCGCAAGACAGAGAAGGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUUUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAACCUGCUAACUAGUCUGCUUGUAAAUAACAGGUUGUACUUCUUAGAGGGACUAUUGUGCAAUAAGCCAAUGGAAGUUUAAGGCAAUAACAGGUCUGUGAUGCCCCUAGACGUGCUCGGCCGCACGCGCGUUACAAUGACUGGCGCAAAAAGUAUUUCCUGUCCUGGGAAGGUACGGGUAAUCUUAUUAAUACCAGUCGUGUUAGGGAUAGUUCUUUGGAAUUGUGGAUCUUGAACGAGGAAUUUCUAGUAAGUGCAAGUCAUCAGCUUGCGUUGAUUAUGUCCCUGCCGUUUGUACACACCGCCCGUCGCUUGUAGUAACGAAUGGUCUGGUGAACCUUCUGGACUGCGACAGCAAUGUUGCGGAAAAAUAAGUAAACCCUACCAUUUGGAACAACAAGAAGUCGUAACAAGGUAUCUGUAGGUGAACCUGCAGAUGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq new file mode 100644 index 0000000..627b884 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.T.violacea.1.seq @@ -0,0 +1,2 @@ +>d.16.e.T.violacea.1 +CACCUGGUUGAUCCUGCCAGUGGUAUAUGCUUGUCUCAAGGACUAAGCCAUGCAAGUGUAAGUAUAAGUAAUUUUUACGACGAAACUGCGAAUGGCUCGGUAAAACAGCUAUAGUUUCUUCGAUGCUAACUUACUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCCAACACGCGGGGCAACCCGUGGUACCAAUUAGAUAUCAAGCCAACAUAUGGUGAUUCAUGAUUGUUUUUCUGAUCGCACGCGCAGUGCGACGCAUCGUUCAAGUUUCUGACCUAUCAACUUUCGAUGGUAAGGUAUUGUCUUACCAUGGUUGUGACGGGUAACGGACCGUGGGUGCGGGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUAACACAGGGAGGUAGUGACAAGAAAUAUCAAUAGAGGGCGUUUCUACGUCUUCUAAUUGGAAUGAGAACAAGGUAAACAGCUUAUCGAGGAUCCAGCAGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCUGUAAGCGUAUACCAAAGUUGUUGCAGUUAAAACGCUCGUAGUCGGAUUUUGGCGCGGCCGGCGCUGUGCGCGUAAAUGCGUGCGGCGUUAAAGAAAAAAUUUAUUUUUUUUCGGGCGUGCUUUUGUGGAGGGCGACACGUGGUGGCUUGAUUGUUGCUGCGGGUCGGCGCCACUUUUUACUGUGAAAAAAUUAGAGUGUUCAAAGCAGGCGUUUGUCGUGAAUACGUUAGCAUGGGAAAAUGGAAUAGGACUUGGUUUCUAUUUUGUUGGUUUGUGAGAGCCGAGUAAUGAUUAAGAGGGACGGUUGGGGGCAUUUGUAUUCCGGCGUCAGAGGUGAAAUUCUUGGAUUGCCGGAAGACAAACCGCUGCGAAAGCGUCUGCCAAGGACGUUUUCAUUGAUCAAGAACGAAAGUAAGGGGAUCGAAGACGAUCAGAUACCGUCGUAGUCUUUACUAUAAACGAUGAGAACUGGGGAUCGGGCGAGCAUUACGAUGACUCGUCCGGAACCCUCCGGGAAACCAAAGUGUUUGCUUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCAUCACCGGGUGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUUACCAGGUCCGGACAUAGUGAGGAUUGACAGAUUGAGAGCUCUUUCUUGAUUCUAUGGUUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAGCGAGACCUGGGCGUGCUAACUAGGGGCUGUUACACAUGUUUGUGUAGCUCAGAAGCAAUAGAGGUUUUUUCUUUUCUUUUCUUUUCUUUCUUUUUUUCCUUUGAGCAAUUGAAGGGGGAGAGGUUUGAAAAAGGAAUGGAACGGAGACUCCUUACUCAUGUUGUUUUGUGCUCCUUCUUAGACGGACUGCGGGCGUCUAGUCCGCGGAAGCUCCAGGCAAUAACAGGUCUGAGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAGCGGACCAACGGGUUUGGAUGCGCGAGAGCGUUUCCUAAUCCCUAAAUCCGCUCGUGCUGGGGAUAGAGGCUUGCAAUUUUCCCUCUUGAACGAGGAAUACCUUGUAAGCGUGGGUCAUCAGCCCGCGCUGAAUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAGUGAUCCGGUGAGGCUUUGGGAUUGCUGCGAUCGGAGUGUUUACGCUCUGGCCGCGGUGAAAACUUAUCCGAACCUUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAAGCU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq new file mode 100644 index 0000000..f847076 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.gallina.seq @@ -0,0 +1,2 @@ +>d.16.e.U.gallina +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGUUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUGAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCCCGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAAGCCUAUGUUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCAUAUAUUAAAUUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCUCGUUCGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCCUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCGCGUUUUAUCCGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUCUCGAUUGAAUCCGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGUGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCUUUGGAAUUAUAGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGUGGGGUCUCGUGCCUCGUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq new file mode 100644 index 0000000..8506647 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.grandis.seq @@ -0,0 +1,2 @@ +>d.16.e.U.grandis +AACCUGGUUGAUCCUGCCAGUAGUCAUACGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAUGAUAUACAGUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCAAAUUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUCAAGGAAAGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUCGUGUCUAUUGUGAUGAUUCAUAAUAACUGAUCGAAUCGCAUAGUCUUUGGCUGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUAACGGGUGACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUAAUUCAGGGAGGUAGUGACAAGAAAUAACGGACUGAGCCUUUGGUUCAGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACCAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGAGGGGGUGACAAAGUCCGCUGAUGCGUGUGCUGCGUCGCCCCUUCAUCCUUCUGUUAACGUUUCUUGGUAUUCAGUUACUGGUUUCGGGCUCAGAUAUUUUACCUUGAGAAAAUUAGAGUGUUUCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUGGGUCUCCUUUGUUGGUUUGAGGGACUCUAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGUGUGUAUUAUCCACCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUUAUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUACUAACUAGUCAACGCAAUCUUAUUGCAUUUGACUUCUUAGAGGGACUUUGUGAUUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGAUGCAUACAGCGAGUACUUUCCAGCUCCGAGAGGCUGCUGGUAAUCAGCAAUAUGCAUCGUGCUUGGGAUUGAUCUUUGGAAUUAUAGAUCAUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUUAGCUUGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUUCGGUGAACCUUUUGGACAGCGUUAGUUUCGGCUGAUGCUGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq new file mode 100644 index 0000000..e4d1fb5 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.maydis.seq @@ -0,0 +1,2 @@ +>d.16.e.U.maydis +UACCUGGUUGAUUCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUCUAAGUAUACGCAAAUUAUACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUAUUUGAUGUUUCUUGCUACAUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCGUAAAAAGCCCCGACUUCUGGAAGGGGUGUAUUUAUUAGAUAAAAACCAUCCUCCUCGGAGUUUGGUGAUUCAUAAUAACUUCUCGAAUCGCACGGCCUUGUGCUGGCGAUGCUUCAUUCAAAUAUCUGCCCUAUCAACUGUCGAUGGUAGGAUAGAGGCCUACCAUGGUUGCAACGGGUAACGGGGAAUAAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCCGACACGGGGAGGUAGUGACAAUAAAUAACAAUGCAGGGCCCUUUUGGGUCUUGUAAUUGGAAUGAGUACAAUUUAAAUCCCUUAACGAGGAACGAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGAAGUUUGGUCUCGGACGCUGGGUCUGCUUAAUUGCAUGUACUUGACGGUCCGAGACUUCCUUCUUGGUGAACGGCCGCCCUCGGGUGGUCCGGAACCAGGACUAUUACUUUGAAAAAAUUAGAGUGUUCAAAGCAGGCCAUAGGCCCGAAUAUAUUAGCAUGGAAUAACAGAAUAGGACGUGCGGUUCUAUUUUGUUGGUUUCUAGAACUGCCGUAAUGAUUAAAAGGGACAGCCGGGGGCAUUAGUAUUUGCACGCUAGAGGUGAAAUUCUUGGAUUGUGCAAAGACUUCCUACUGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAGGUUAGGGUAUCGAAAACGAUUAGAUACCGUUGUAGUCUUAACAGUAAACUAUGCCGACUCCGAAUCGGUCGAUGCUCAUUUCACUGGCUCGAUCGGCGCGGUACGAGAAAUCAAAGUUUUUGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGAAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAAACUCACCGGGUCCGGACAUAGUAAGGAUUGACAGAUUGAUGGCGCUUUCAUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACCUUGACCUGCUAAAUAGACGGGUUGACAUUUUGUUGGCCCCUUAUGUCUUCUUAGAGGGACAAUCGACCGUCUAGGUGAUGGAGGCAAAAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCCGGGCUGCACGCGCGCUACACUGACAGAGACAACGAGUGGAGCCCCUUGUCCGAAAUGACUGGGUAAACUUGUGAAACUUUGUCGUGCUGGGGAUGGAGCUUUGUAAUUUUUGCUCUUCAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCAGCUUGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGAAUGGCUUAGUGAGGACUUGGGAGAGUACAUCGGGGAGCCAGCAAUGGCACCCUGACGGCUCAAACUCUUACAAACUUGGUCAUUUAGAGGAAGUAAAAGUCGUAACAAGGUAUCUGUAGGUGAACCUGCAGAUGGAUCAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq new file mode 100644 index 0000000..7e0d307 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.U.pisces.seq @@ -0,0 +1,2 @@ +>d.16.e.U.pisces +AACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGACUAAGCCAUGCAUGUCUAAGUAUAAAGGUUAUACAAUGAAACUGCGAAUGGCUCAUUAAAACAGUUAUAGUUUAUUUGAUAAUCGAAAUUACAUGGAUAACCGUGGUAAUUCUAGAGCUAAUACAUGCUGGUUAGCCUGACUUUUAGGAAGGGCUGUAUUUAUUAGAUAACAAACCAAUAUUCCUUGUGUCUAUUGUGACGACUCAUAAUAACUGAUCGAAUCGCAUGGACUUUGUCCGCGAUACAUCAUUCAAGUUUCUGCCCCAUCAGCUUUCGAUGGUAGUGUAUUGGACUACCAUGGCUUUCACGGGUAACGGAGGAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCUAAGGAAGGCAGCAGGCGCGUAAAUUACCCAAUCCUGACUCAGGGAGGUAGUGACAAGAAAUAACGGACCGAGGCUAUGCUUCGGGAUUGCAAUGAGUAGAAUUUAAACCCCUUUACGAGGAUCAAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGAUUUCUGGGAGGGUGCCAAUGUCCGCAUGUUGCGUGUGCAGCGGCGCCCUUCCAUCCUUCUGUUAACGUUUCUGGUAUUCAGUUACUGGACUCGGGCUCAGAUACUUUACCUUGAGAAAAUUAGAGUGUUCCAGGCAGGCUUGCGCCGGAAUACAUUAGCAUGGAAUAAUAGAAUAGGACUUUAGUCUCCUUUGUUGGUUUGAGGGACUGAAGUAAUGAUUAAUAGGGAUAGUUGGGGGCAUUAGUAUUUAAUUGUCAGAGGUGAAAUUCUCGGAUUUGUUAAAGACUAACUUAUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUAGGGGAUCAAAGACGAUCAGAUACCGUCGUAGUCUUAACCAUAAACUAUGCCGACUAGGGAUCGGAGGCUCGUUUUAUCAGCCUUCGGCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCUGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCUUGCGGCUCAAUUUGACUCAACACGGGAAAACUUACCAGGUCCAGACAUAGUGAGGAUUGACAGAUUGAUAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGUGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUUAGCCUGCUAACUAGUCGACUCAAUCUCGAUUGGGAACGACUUCUUAGAGGGACUUUGUGACUAAACACAAGGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCUGGGCCGCACGCGUGCUACACUGACGCAUACAGCGAGUACUUCCCAGCUCCGAGAGGCAGCUGGUAAUCAGCAAUAUGCGUCGUGAUGGGGAUAGAUCCUUGGAAUUAUGGAUCUUGAACGAGGAAUUCCUAGUAAGCGCAAGUCAUCACCUUGCGCUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUUCGAGUGAUCCGGUGAACCUUUUGGACUGCGGGUGGCUUCGUGCCAACUGUGGAAAAUCAAGUAAACCAUAUCACUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCAGAAGGAUCAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq new file mode 100644 index 0000000..9cf06ee --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.acridophagus.seq @@ -0,0 +1,2 @@ +>d.16.e.V.acridophagus +CACCAGGUUGAUUCUGCCUGUUAUAUGUACUAGUGUCGAAGAUUUAGCCAUGCAUGCUUUACGAAUUCACAAGAAGAAGUGGCGGACAGCUCAGUAAUACAGUUAUAAUAUACUCUCUACUAAAGGAUAACCGCGGUAAGCUGCGGGUAAAACUUCAAGCUAUGUGUUUCAUGAAAGAAUUUAUAGUUCAGAGUGUUAGUUUCUGGCCUAUUAGUUAGUAGGUAAUGUAAGGGAUUACCUAGACUAUUAUGGGUAACGGGAGAUGAAUGUCUGAUACCGGAGAGGAAGCCUUAGAAACCGCUUUCACGUCCAAGGAUGGCAGCAGGCGCGAAACUUACCCAAUCGUUUUUUAAGACGGAGGUAGUUAUGACACAUGUGAAUUAUUCACGAGGAAGAUCAAUAAAUCAGAUUUUUUUUACUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAGUAGUGCAUAUACAUGCUGUAGUUAGAAAGUUUGUAGCCGUAUAAGCUUGAAUCAGAGGAAAGGAGGACUCUUAAGGUAAACUUUAACUCUGGUCAAUGCUUAUAUUCGAAGCGGAUGGAGGCACUUGUAUUCAAUAGCGAGAGGUAAAAUUUGAUGACCUAUUGAGGACAAUCAGUAGCGAAAGCGAGUGUCUAGUACGCGUUUGAGGGUCAAGAACGUUAGCCGGAGGAUCGAAGAUGAUUAGAUACCGUUGUAGUUCCGGCCGUAAACCAUGCCUACUUGCCUUGUACAUAGUAUGAAGCAUAGAGAAAUUAAGAGUUUUUGGGCUCUAGGGAUAGUAAUCCGGCAACGGACAAACUUAAAGAAAUUGGCGGAAGGACACCACAAGGAGUGGAUUGUGCGGCUCAACUUGACUCAACACGGGAAAUCUUACCAGGGUCUGUAUAUGUGAGACUGUCCCAUUUAUGGUGGUACACGAUAAUAUACUGAGUGGUGCAUGGCCGUUUUCAACACGUGGGGUGACCUGUCAGGUUUAUUCCGGUAACGUGUGAGGUCACAGUAUUAAUAAGUAUUUUAAUAGACAGCUAAUGGUAAAUUAGAGGAAGUGUGACGAUAACAGGUCAGUGAUGCCCUUAGAUACCCUGGGCUGCACGCGCAAUACAUUGAGUAAGUCAUUUACAAUAGUAAUUUUGAAACUUACUCGCUACUGGGAUCAUCCUUUGUAAUUGGGAUGUGAACGUGGAAUUCCUAGUAAUCGUAGCUCACUAAGUUACGAUGAAUGUGUCCCUGUUCUUUGCACACACCGCCCGUCGCUAUCUAAGAUGGAUGUUGAUAUGAAAUUGCUGCUUGAAUGUGAGGUACUUGAGUAUUAACAACUAGAUAAGAUAUAAGUCGUAACAAGGCUGCUAUAGAAGAAUCUGUGGCAAGAUCAUAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq new file mode 100644 index 0000000..b9bf68b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.corneae.seq @@ -0,0 +1,2 @@ +>d.16.e.V.corneae +CACCAGGUUGAUUCUGCCUGACGUAGAUGCUAGUCUCUAAGAUUAAGCCAUGCAUGUUUCCUCAAUCAGGGACGAAUAGCUCAGUAAAACUGCGAUGAUUUAGUCUGGCUGUGUAGAUAACACGUGAAAAUGUAGCUAAGGGAAGGCAGAAUAAGACGCAGGACUAUCAGUUAGUUGGUAGUGUAAUGGACUACCAAGACAGUGACGGUUGACGGGAAAUUAGGGUUUUGUACCGGAGAGGGAGCCUGAGAGAUUGCUCCCACGUCCAAGGACGGCAGCAGGCGCGAAAAUUGCCCACUCUUUGCAGGAGGCAGUUAUGAGACGUGAAGAUGAGUAUCUUGUAAAGAGGGAUAGGAGAAUUGGAGGGCAAGUUUGGUGCCAGCAGCCGCGGUAAUACCGACUCCAAGAGUGUGUAUGAGAGAUGCUGCAGUUAAAAAGUCCGUAGUCAUAGAAGGGCAAAGAGAGAUGCGAGGUCUCACAGUGCGAUGAUGGAGGAGCCGAUGGGGAACAUAGUAUACCAGGGCGAGAGAUGAAAUGCCAAGACCCCUGGUGGACUGAGCGAGGCGAAGGCGAUGUUCUUGUAGGCAUUCGGUGAUCAAGGACGAAGGCUGGAGUAUCGAAAGUCAUUAGAUACCGCAGUAGUUCCAGCAGUAAAAGAUGCCGACAUGCUCAUUGGACACAGUGGGCAGGGAGAAAUCUUAGAGUUCGGGCUCUGGGGAUAGUAUGCUCGCAAGGGUGAAAAUUAAAGAAAUUGACGGAGCUACACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGAAACUUACCAGGGCCAAGUACUUGUGUAGAAACGAGCAAUACAGGAGUGGUGCAUGGUCGUUGGAAAUUGAUGGGAUGACUUUGACCUUAAAUGGUUGAAUGAGUGAGAUCUUUUGGACAUGUUCCGCACGGAACAGGAAGGAAAAGGCUAUAACAGAUCCGAGAUGCCCUCAGAUGCCCUGGGCUGCACGCGCAAUACAAUAGCAGGUAGAGAGAGAGACAGGAAGGUGCUCAGAUGGACUAUGUGCUGUAAGGCACAUACGAAAGAGGAAUUCCUAGUAAGUGUGUAUCAACAAUGGAUAUUGAAUAAGUCCCUGUAGCUUGUACACACCGCCCGUCACUAUCUCAGAUGUUUUUCAGGAUGAAGAGUCCAGGCUCUGAAUAAUGAAAAGUAGAUAAGAUGUAAGUCGUAACAAGGUUGCGGUUGGUGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq new file mode 100644 index 0000000..32ce19a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.culicis.seq @@ -0,0 +1,2 @@ +>d.16.e.V.culicis +CACCAGGUUGAUUCUGCCUGACGUGGAUGCUAGUCUCAUAGGUUAAGCCAUGCAUGUGCAAGCGAAGCCGGUGGUGGAGCGGCGCAAGGCUCAGUAACGGGCGACUGAUUUGAUCUCCCGGUGUGGACAACCUCUAUAACCGGAGGCCAAAACACAGGAGGCGCGUGACACGGGCACGGGCGUGCAACCGGCAGGUGCGGGAGAGUAAGGAGCCAUCCCAUCAGUUAGUAAGUAGGGUAAGGGCCUACUUAGACGAAGACGGGUACGGGGAAUUAGAGUUCGAUUCCGGAGAGGGAGCCUGAGAGACGGCUACCAGGUCCAAGGACAGCAGCAGGCGCGGAAAUUACCGAAGCCCGCGUUCGGGGCGGUAGUAAGGAGACGUGAAUACGAUGUGCAGGUAAAAUAUGCACUGGUAACAGGAGGUCAAGACUGGUGCCAGCAUCCGCGGUAAUACCAGCUCCUGGAGUGUCUAUGACGAUUGUUGCAGUUAAAGAGUUCGUAGUCGGGCUGCAUGACCGGCGCUGAAGGCUCCCUAUCGAGGGGGGCAGGGCGCCGGAAAAGCAGAGGAUGAGGAGCGGCCGGGGGCCAGGUUAUUAAGCGACGAGAGGUGAAAUUUGAUGACUCGCUUAGGAGCAGCAGAGGCGAAAGCGCUGGCCAGGGGCGAAUCCGAUGAUAAAGGACGUAGGCUAGAGGAUCGAAGACGAUUAGAGACCGUUGUAGUUCUAGCAGUAAACGAUGCCGAUGCCGUGGGGCGGUGCAGCCGCCACGCGGAGGAGAAAUUGAGUAGGGCCCUGGGGAGAGUACACGCGCAAGCGGGAAAUUUAAAGGAAAUUGACGGAAGAACACCACAAGGAGUGGAGUGUGCGGCUUAAUUUGACUCAACGCGGACAGCUUACCAGGCCCGACGGUCGCACGAGUGUGGUACACGAUAGGCCGGAGAGUGGUGCAUGGCCGUUAACGACAAGUGGGGUGACCUUUGGGUUAAGUCCGGGAAGUAGUGAGACCCCUGCCGGCGCGCCGGGACAGGUGCUCAAAGCACAGGAAGGAAGGGUCAAGAACAGGUCAGUGAUGCCCUUAGAUGGUCUGGGCUGCACGCGCACUACAGUGGUCGCAGAAAUCAGUGCCCGAGCGGCAAUGGCGAUCGAGAGGGAACGAGCUCUGGAAGGGGCUCGGGAACGAGGAAUUGCUAGUAAUCGUGGGCUCAUUAAGACACGGUGAAUACGUCCCUGUUCUUUGUACACACCGCCCGUCGUUAUCGAAGAUGGAGUCAGGCGCGAACAAGCGAGAGCGAGUGAGUGCAGGGUUCUAGAUGUGAUACAAGUCGUAACAAGGUAGCUGUAGGAGAACCAGUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq new file mode 100644 index 0000000..ddad56b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.imperfecta.seq @@ -0,0 +1,2 @@ +>d.16.e.V.imperfecta +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUACUCUAAGAUUAACCCAUGCAUGUUAUUGAAUAUAAAGAAAAGACGAACAGCUCAGUAACUCUUAUUUGAUUUGAUGUAUUAGGACUCUAACUAUGUUAAAUUAUAGGUAACAAUAAUACAAUAAGAAUAAGAUCUAUCAGUUAGUUGUUAAGGUAAUGGCUUAACAAGACUAUGACGGAUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGAUUGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGAUAUUAUAUUGAGGCAGUUAUGAGUAGUAUUUUAUAAUUAUUGUAAUAUUGUAAGUACAUAUUACAAGAUAAAUCGGAGGGCAAAUCGAGUGCCAGCAGCCGCGGUAAUACUUGUUCCGAUAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCUGUAGUUUAUUUAUAAUAAGCAUUGUAAGGUAUACUGUAUGGUUAGGAGAGAGAUGAAAUGUGAUAACCCUAACUGGAUGAACAGAAGCGAAAGCUGUAUACUUAAAUGUAUUAUUAGAACAAGGACGUAAGCUAGAGGAUCGAAGAUGAUUAGAUACCAUUGUAGUUCUAGCAGUAAACUAUGUUGAAUCAUAGAUAUAUUUUGAUAUAUAUUUGUGUAGAGAAAUUAAGAUUAUAUUGACUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGGGGUAAUUUACCAGGUAUAACAUGGUAUAAUAUUUUAUCAUGAUAGUGGUGCAUGGCCGUUUCCAAUGGAUGCUGUGAAGUAAUGAUUAAUUUCAACAAGAUGUGAGACCCUCAUUUAGACAGAUGUAGUGAUACAUAUGAAGGAGAGGAUUAAAACAGGUCCGUUAUGCCCUAAGAUAAUCUGGGUUGCACGCGCAAUACAAUAAUAUUUGAUAUUAUAAGGGAUAAUAUAAUGUAAGAUAUAUUUGAACAUGGAAUUGCUAGUAAAUUUUAUUUAAUAAGUAGAAUUGAAUGAGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGGUAUUAUCUAUGAACAAAUUUAUAAAGUGAAUAGAUAGUACUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAGCAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq new file mode 100644 index 0000000..1ae37da --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.V.necatrix.seq @@ -0,0 +1,2 @@ +>d.16.e.V.necatrix +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUUCCCUAAGAUUAACCCAUGCAUGUUUUUGAUAUGGAAAAAUGGACUGCUCAGUAAUACUCACUUUAUUUAAUGUAUUAAAUUAGUAUAACUGCGUUAAAGUGUAGCAUAAGACAUAUACAGUAAGAGUGAGACCUAUCAGCUAGUUGUUAAGGUAAUGGCUUAACAAGGCAAUGACGGGUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGGAUUUUAUCUGAGGCAGUUAUGGGAAGUAAUAUUCUAUUGUUUCAUAUUGUAAAAGUAUAUGAGGUGAUUAAUUGGAGGGCAAAUCAAGUGCCAGCAGCCGCGGUAAUACUUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUUAUAUUUAAGAAGCAAUAUGAGGUGUACUGUAUAGUUGGGAGAGAGAUGAAAUGUGACGACCCUGACUGGACGAACAGAAGCGAAAGCUGUACACUUGUAUGUAUUUUUUGAACAAGGACGUAAGCUGGAGGAGCGAAGAUGAUUAGAUACCAUUGUAGUUCCAGCAGUAAACUAUGCCGACGAUGUGAUAUGAUAUUAAUUGUAUUAGAUGAUAGAAAUUUGAGUUUUUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCAGAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGUAACUUACCAAUAUUUUAUUCAGAGAAGAUUUUCGAUCUGAGAAUGAUAAUAGUGGUGCAUGGCCGUUUUCAAUGGAUGCUGUGAAGUUUUGAUUAAUUUCACCAAGACGUGAGACCCUUUUAUUAAUAGACAGACACAAUCAGUGUAGGAAGGAAAGGAUUAAAACAGGUCCGUUAUGCCCUCAGACAUUUUGGGCUGCACGCGCAAUACAAUAGAUAUAUAAUCUUUAUGGGAUAAUAUUUUGUAAGAGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAUUAAAUAAGUAGAAUUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGAUAUGUGUUGUGAAAUUAGUGAAAACUACUUGAACAAUAUGUAUUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq new file mode 100644 index 0000000..ae6d794 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Vairimorpha.sp.C21.seq @@ -0,0 +1,2 @@ +>d.16.e.Vairimorpha.sp.C21 +CACCAGGUUGAUUCUGCCUGACGUAGACGCUAUUCCCUAAGAUUAACCCAUGCAUGUUUUUGACAUUUGAAAAAUGGACUGCUCAGUAAUACUUACUUUAUUUAAUGUACAUUUGAAAAUAACUACGUUAAAGUGUAGAUAAGAUGUGUACAGUAAGAGUAAGACCUAUCAGCUAGUUGUUAAGGUAAUGGCUUAACAAGGCAGUGACGGGUAACGGUAUUACUUUGUAAUAUUCCGGAGAAGGAGCCUGAGAGACGGCUACUAAGUCUAAGGAUUGCAGCAGGGGCGAAACUUGACCUAUGGAUUUUUUCUGAGGCAGUUAUGGGAAGUAAUAUUAUAUUGUUUCAUAUUGUAAAAGUAUAUGAGGUGAUUAAUUGGAGGGCAAAUCAAGUGCCAGCAGCCGCGGUAAUACUUGUUCCAAGAGUGUGUAUGAUGAUUGAUGCAGUUAAAAAGUCCGUAGUUUAUGAUUAAGAAGCAAUAUGAGGUGUACUGUAUAGUUGGGAGAAAAAUGAAAUGUGACGACCCUGACUGGACGAACAGAAGCGAAAGCUGUACACUUGUAUGUAUUUUUUGAACAAGGACGUAAGCUGGAGGAGCGAAGAUGAUUAGAUACCAUUGUAGUUCCAGCAGUAAACUAUGCCAACGAUGUGAUAUGAUAUUAAUUGUAUUACAUGAUAGAAAUUUGAGUUUUUUGGCUCUGGGGAUAGUAUGAUCGCAAGAUUGAAAAUUAAAGAAAUUGACGGAAGAAUACCACAAGGAGUGGAUUGUGCGGCUUAAUUUGACUCAACGCGAGGUAACUUACCAAUAUUUUAUUAUUCUGAGAUAAUUUUCCAAUUUGAGAAUGAUAAUAGUGGUGCAUGGCCGUUUUCAAUGGAUGCUGUGAAGUUUUGAUUAAUUUCAACAAGACGUGAGACCCUUUUUUAUAUAAGACAGACACAAUCAGUGUAGGAAGGAAAGGAUUAAAACAGGUCCGUUAUGCCCUCAGACAUUUUGGGCUGCACGCGCAAUACAAUAGAUAUAUAAUCUUUAUGGGAUAAUAUUUUGUAAGAGAUAUUUGAACUUGGAAUUGCUAGUAAAUUUUAUUAAAUAAGUAGAAUUGAAUGUGUCCCUGUUCUUUGUACACACCGCCCGUCGCUAUCUAAGAUGAUAUGUGUUAUGAAAAUAGUGAAAACUACUUGAACAAUAUGUAUUAGAUCUGAUAUAAGUCGUAACAUGGUUGCUGUUGGAGAACCAUUAGCAGGAUCAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq new file mode 100644 index 0000000..780471c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.borealis.seq @@ -0,0 +1,2 @@ +>d.16.e.X.borealis +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCACGUGUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGAUCGCUCCAUCUGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGAGCGCUGACCCCCAGGGAUGCGUGCAUUUAUCAGAUCAAAACCAACCCGGGGCCCCCGCGCCCCGGCCGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGUCCCCGUGACGGCGACGAUACAUUCGGAUGUCUGCCCUAUCAACUUUCGAUGGUACUUUCUGCGCCUACCAUGGUGACCACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACGCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACGAGGAUCUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAUCGAGCUGGCGGUCCGCCGCAAGGCGAGCUACCGCCUGUCCCAGCCCCUGCCUCUCGGCGCCUCCCCGAUGCUCUUGACUGAGUGUCCCGGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCCAAGCAGGCCGCGUCGCCUGGAUACUUCAGCUAGGAAUAAUGGAAUAGGACUCCGGUUCUAUUUUGUUGGUUUUCGGAACUGGGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGUGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGAACCAAAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUAGCGAUCCGGCGGCGUUAUUCCCAUGACCCGCCGAGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGAAAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCCUCCAUGCUAACUAGUUACGCGACCCCCGGCGGUCGGCGUCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACACGAGAUCGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGAACGGAUCAGCGUGUGUCUACCCUGCGCCGACAGGUGCGGGUAACCCGCUGAACCCCGUUCGUGAUAGGGAUCGGGGAUUGCAAUUAUUUCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUCGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGUCCUCGGAUCGGCCCCGCCGGGGUCGGCAACGGCCCUGGCGGAGCGCCGAGAAGACGAUCAAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq new file mode 100644 index 0000000..ec9c5bb --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.X.laevis.seq @@ -0,0 +1,2 @@ +>d.16.e.X.laevis +UACCUGGUUGAUCCUGCCAGUAGCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCACGUGUAAGUACGCACGGCCGGUACAGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUGGUUCCUUUGAUCGCUCCAUCUGUUACUUGGAUAACUGUGGUAAUUCUAGAGCUAAUACAUGCCGACGAGCGCUGACCCCCAGGGAUGCGUGCAUUUAUCAGACCAAAACCAAUCCGGGGCCCCCGCGCCCCGGCCGCUUUGGUGACUCUAGAUAACCUCGGGCCGAUCGCACGUCCCCGUGACGGCGACGAUACAUUCGGAUGUCUGCCCUAUCAACUUUCGAUGGUACUUUCUGCGCCUACCAUGGUGACCACGGGUAACGGGGAAUCAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCACUCCCGACGCGGGGAGGUAGUGACGAAAAAUAACAAUACAGGACUCUUUCGAGGCCCUGUAAUUGGAAUGAGUACACUUUAAAUCCUUUAACGAGGAUCUAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUAAAGUUGCUGCAGUUAAAAAGCUCGUAGUUGGAUCUUGGGAUCGAGCUGGCGGUCCGCCGCGAGGCGAGCUACCGCCUGUCCCAGCCCCUGCCUCUCGGCGCCUCCCCGAUGCUCUUGACUGAGUGUCCCGGGGGCCCGAAGCGUUUACUUUGAAAAAAUUAGAGUGUUCCAAGCAGGCCGCGUCGCCUGGAUACUUCAGCUAGGAAUAAUGGAAUAGGACUCCGGUUCUAUUUUGUUGGUUUUCGGAACUGGGGCCAUGAUUAAGAGGGACGGCCGGGGGCAUUCGUAUUGUGCCGCUAGAGGUGAAAUUCUUGGACCGGCGCAAGACGAACCAAAGCGAAAGCAUUUGCCAAGAAUGUUUUCAUUAAUCAAGAACGAAAGUCGGAGGUUCGAAGACGAUCAGAUACCGUCGUAGUUCCGACCAUAAACGAUGCCGACUAGCGAUCCGGCGGCGUUAUUCCCAUGACCCGCCGAGCAGCUUCCGGGAAACCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUUGCAAAGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGAGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGAAACCUCACCCGGCCCGGACACGGAAAGGAUUGACAGAUUGAUAGCUCUUUCUCGAUUCUGUGGGUGGUGGUGCAUGGCCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGAUAACGAACGAGACUCCUCCAUGCUAACUAGUUACGCGACCCCCGGCGGUCGGCGUCCAACUUCUUAGAGGGACAAGUGGCGUUCAGCCACACGAGAUCGAGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUCCGGGGCUGCACGCGCGCUACACUGAACGGAUCAGCGUGUGUCUACCCUGCGCCGACAGGUGCGGGUAACCCGCUGAACCCCGUUCGUGAUAGGGAUCGGGGAUUGCAAUUAUUUCCCAUGAACGAGGAAUUCCCAGUAAGUGCGGGUCAUAAGCUCGCGUUGAUUAAGUCCCUGCCCUUUGUACACACCGCCCGUCGCUACUACCGAUUGGAUGGUUUAGUGAGGUCCUCGGAUCGGCCCCGCCGGGGUCGGCCACGGCCCUGGCGGAGCGCCGAGAAGACGAUCAAACUUGACUAUCUAGAGGAAGUAAAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq new file mode 100644 index 0000000..6dcff46 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.e.Z.mays.seq @@ -0,0 +1,2 @@ +>d.16.e.Z.mays +UACCUGGUUGAUCCUGCCAGUAGUCAUAUGCUUGUCUCAAAGAUUAAGCCAUGCAUGUGCAAGUAUGAACUAAUUCGAACUGUGAAACUGCGAAUGGCUCAUUAAAUCAGUUAUAGUUUGUUUGAUGGUACGUGCUACUCGGAUAACCGUAGUAAUUCUAGAGCUAAUACGUGCAACAAACCCCGACUUCCGGGAGGGGCGCAUUUAUUAGAUAAAAGGCUGACGCGGGCUCUGCCCGCCGAUCCGAUGAUUCAUGAUAACUUGACGGAUCGCACGGCCUUCGUGCCGGCGACGCAUCAUUCAAAUUUCUGCCCUAUCAACUUUCGAUGGUAGGAUAGGGGCCUACCAUGGUGGUGACGGGUGACGGAGAAUUAGGGUUCGAUUCCGGAGAGGGAGCCUGAGAAACGGCUACCACAUCCAAGGAAGGCAGCAGGCGCGCAAAUUACCCAAUCCUGACACGGGGAGGUAGUGACAAUAAAUAACAAUACCGGGCGCGUUAGUGUCUGGUAAUUGGAAUGAGUACAAUCUAAAUCCCUUAACGAGGAUCCAUUGGAGGGCAAGUCUGGUGCCAGCAGCCGCGGUAAUUCCAGCUCCAAUAGCGUAUAUUUAAGUUGUUGCAGUUAAAAAGCUCGUAGUUGGACCUUGGGCCGGGCCGGGUGCCGCCGCCGUACGGGCAGAACCGACCGGCUCGACCCUUCUGCCGGCGAUGCGCUCCUGGCCUUAACUGGCCGGGUCGUGCCUCCGGGCCGUUACUUUGAAGAAAUUAGAGUGCUCAAAGCAAGCCAUCGCUCUGGAUACAUUAGCAUGGGAUAACAUCAUAGGAUUCCGGUCCUAUUGUGUUGGCCUUCGGGAUCGGAGUAAUGAUUAAUAGGGACAGUCGGGGGCAUUCGUAUUUCAUAGUCAGAGGUGAAAUUCUUGGAUUUAUGAAAGACGAACAACUGCGAAAGCAUUUGCCAAGGAUGUUUUCAUUAAUCAAGAACGAAAGUUGGGGGCUCGAAGACGAUCAGAUACCGUCCUAGUCUCAACCAUAAACGAUGCCGACCAGGGAUCAGCGGUGUUACUAAUAGGACCCCGCUGGCCACCUUAUGAGAAAUCAAAGUCUUUGGGUUCCGGGGGGAGUAUGGUCGCAAGGCUGAAACUUAAAGGAAUUGACGGAAGGGCACCACCAGGCGUGGAGCCUGCGGCUUAAUUUGACUCAACACGGGGAAACUUACCAGGUCCAGACAUAGCAAGGAUUGACAGACUGAGAGCUCUUUCUUGAUUCUAUGGGUGGUGGUGCAUGGUCGUUCUUAGUUGGUGGAGCGAUUUGUCUGGUUAAUUCCGUUAACGAACGAGACCUCAGCCUGCUAACUAGCUAUGCGGAGCCAUCCCUCCGUAGUUAGCUUCUUAGAGGGACUAUGGCCGUUUAGGCCGCGAAGUUUGAGGCAAUAACAGGUCUGUGAUGCCCUUAGAUGUUCUGGGCCGCACGCGCGCUACACUGAUGUAUCCAACGAGUAUAUAGCCUUGGCCGACAGGCCGGUAAUCUUGGGAAAUUUCAUCGUGAUGGGGAUAGAUCAUUGCAAUUGUUGGUCUUCAACGAGGAAUGCCUAGUAAGCGCGAGUCAUCAGCUCGCGUUGACUACGUCCCUGCCCUUUGUACACACCGCCCGUCGCUCCUACCGAUUGAAUGGUCCGGUGAAGUGUUCGGAGCUCGGCCGCACCGGUUCGCCGCCCCCGACGUCGCGAGAAGUCCAUUGAACCUUAUCAUUUAGAGGAAGGAGAAGUCGUAACAAGGUUUCCGUAGGUGAACCUGCGGAAGGAUCAUUG diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq new file mode 100644 index 0000000..3994c56 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.americana.seq @@ -0,0 +1,2 @@ +>d.16.m.A.americana +CAUAGGUUUGGUCCCAGCCUUCCUAUUGACUACUAAUAGACUUACACAUGCAAGCAUCCGCACCCCAGUGAAGACGCCCUUUAAAUCCACCUGAACCAAAAGGAGCUGGUAUCAAGCACACAUUUGUAGCUUAUGACGCCUUGCUCAGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAGCUAUGGACGAAAGUCUGACUAAGUCAUAUUGAUAAGGGUCGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCUAGUUAAUAGGAAUACGGCGUAAAGAGUGUUAAAGCAUCACACUAAAUAGAGUUAAAUUAUAACUAAGCUGUAAAAAGCCACAGCUGUAAUAAAAAUAGACAACGAAAGUGACUCUACAACCGCUGAUCACACUACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCAUAAACACAGGUAAUUGUAUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAAGGAACAAGAGUAAGCAUAAUAAUAGCACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGGGUUGGAAAGAAAUGGGCUACAUUUUCUAUUUCAAGAACACUCAACACGAAAGUUAUUAUGAAACUGAUGACUAAAGGAGGAUUUAGUAGUAAACUAAGAAUAGAGCGCUUAGUUGAAUUAGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAAACACGAUACACCUAAACUUAUUCACACGUAUUAACCGUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq new file mode 100644 index 0000000..487d01e --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.cahirinus.seq @@ -0,0 +1,2 @@ +>d.16.m.A.cahirinus +AAUAGGUUUGGUCCUAGCCUUAUAAUUAGCUGAAAGUAAAAUUACACAUGCAAGACUCCCCACACCAGUGUCAAAUCCCUUAGAACUAGACAGCUAACCUAAGGAGAGGAUAUCAAGCACAUUAAUAUAGCUCAAGACAUCUCGCCAAGCCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCAAUGAACGAAAGUUUGACUUAGUUAUACUUCCAAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUUUUACGGCGUAAAAGGUGUUAUAUCUAAAACAAAUAGAAUUAAAACCUGACUUAUAUGUGAAAAUUCAUUGUCAGACAAAAACACAACCACGAAAGUGAUUCUAAUAAACCAAACACGAAAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUAAAUAAUUAAUAACAAAAUUAUUUGCCAGAGAACUACUAGCCAUAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAUACCCCGUUACACCUCACCACCCCUUGCUAAUCCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUCAAAAGGACACACAGUAAGCAAGAGCACAAACAUAAAAAAGUUAGGUCAAGGUGUAGCCCAUGAGGUGGGAAGUAAUGGGCUACAUUUUCUUAAAAAGAACACACGAAACCCUUUAUGAAAUUAAAGGAUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUGCGCACACACCGCCCGUCACCCUCCUCAAACUAAUCUUCAAGUAAAAUAAAUAAAAUUAAACUAACUAGAAUACGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq new file mode 100644 index 0000000..eeb9896 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.A.fulgens.seq @@ -0,0 +1,2 @@ +>d.16.m.A.fulgens +CAAAGGUUUGGUCCUAGCCUUCCCGUUAGUUCUUAAUAAAAUUACACAUGCAAGUAUCUACACCCCAGUGAAAAUGCCCUCCAAAUCACUAGUUGAUUAAAAGGAGCAGGUAUCAAGCACACUUUACAUAAGUAGCUCACAACACCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCUAUAAACGAAAGUUUGACUAAGUUAUAUUAAUAGAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUAACCCAAACUAACGGGCAUCCGGCGUAAAACGUGUUAAAGAAUCUACUCACAUUAAAGUUAAAACUUAAUCAGGCCGUAAAAAGCUACCGUUAACAUAAAAUACCUUACGAAAGUAACUUUAUUAAUUCUGAUUACACGACAGCUAAGGCCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAGUUUAGUAUAACAAAACUAUUCGCCAGAGAACUACUAGCAAUAGCCUAAAACUCAAAGGACUUGGCGGUGCUUUACACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUUACCACUUCUAGCUACUUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUCAAAAGGAAGCAAAGUAAGCAUAAUGAUUCCUGCAUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAAGUGGAAAGAAAUGGGCUACAUUUUCUAAACAAGAACACUAUACGAAAAUUUUUAUGAAAUUAAAACCUAAAGGUGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAGUUGAAUUGGGCUAUAAAGCACGCACACACCGCCCGUCACCCUCCUCAAACGUCAAGAUUUAAACCCAAUAUAUAAUCACAACAGACUAAACGCAAGAGGAGACAAGUCGUAACAAGGUAAGCGUACUGGAAGGUGUGCUUGGAUAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq new file mode 100644 index 0000000..2249b46 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.brevicauda.seq @@ -0,0 +1,2 @@ +>d.16.m.B.brevicauda +UAAAGGUUUGGUCCCAGCCUUCCUAUUAAUUGUUAGCAAAUUUACACAUGCAAGUAUCCGCGCCCCUGUGAGAAUACCCUUUAAAUCACCUAUGACUGAAAGGAGUAGGUAUCAAGCACACUUAUUUAUAAGUAGCUAAUCACACCUUGCUUAGCCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCCAUGAACGAAAGUUCGACUAAGUUAUGCUAAUAUUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGGUAGCGGCGUAAAGCGUGUUAAAGAACACUAAAUAAAAUAAAGAUAAAACUUGACUAGGCUGUAGAAAGCAACAGUCAAGACUAAAAUAAACUACGAAAGUGACUUUAUUACUUUUGAUCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUAGGUAAUUUAAUUAACAAAACUACUCGCCAGAGGACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCGCCCCUUGCUAAUACAGCUUAUAUACCGCCAUCUUCAGCAAACCCUUAAAAGGAAUAACAGUAAGCUUAAAUAUUUCACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGGCGGGAAGAAAUGGGCUACAUUUUCUAUAACUAGAAUAUUCACGAAAGUUUCUAUGAAACUAGAAACCAAAGGAGGAUUUAGUAGUAAGUUAAGAAUAGAGCGCUUAACUGAACCAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAUUUUAAGUCUACUGAUAUAUAAUCUCAGACUAACUAAUAUUAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACGAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq new file mode 100644 index 0000000..f3a2a28 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.B.taurus.seq @@ -0,0 +1,2 @@ +>d.16.m.B.taurus +CAUAGGUUUGGUCCCAGCCUUCCUGUUAACUCUUAAUAAACUUACACAUGCAAGCAUCUACACCCCAGUGAGAAUGCCCUCUAGGUUAUUAAAACUAAGAGGAGCUGGCAUCAAGCACACACCCUGUAGCUCACGACGCCUUGCUUAACCACACCCCACGGGAAACAGCAGUGACAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGUUAUAUUAAUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAGCUAACAGGAGUACGGCGUAAAACGUGUUAAAGCACCAUACCAAAUAGGGUUAAAUUCUAACUAAGCUGUAAAAAGCCAUGAUUAAAAUAAAAAUAAAUGACGAAAGUGACCCUACAAUAGCCGACGCACUAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAGAUAAUUACAUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAAUUCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAAAAAAAGUAAGCGUAAUUAUGAUACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGAAAUGGGAAGAAAUGGGCUACAUUCUCUACACCAAGAGAAUCAAGCACGAAAGUUAUUAUGAAACCAAUAACCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAGAUUCAGUGCAUCUAACCCUAUUUAAACGCACUAGCUACAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq new file mode 100644 index 0000000..ca47b03 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.C.elegans.seq @@ -0,0 +1,2 @@ +>d.16.m.C.elegans +UAAAGUUUUCUUUCAGGGAAUUAAAAUUUGAUCAUGGUUUAAGAUGAUUUAAAAUGGUAUUAUCUAAAUUUGAUUUACAGAGUAGGCAAUAAAAAUUUACCUCGGCAAUUUAUCGCUUGUAAAAUACUUGUUCCAGAAUAAUCGGCUAGACUUGUUAAAGCUUGUACUUUAAUUGAUGUUAAUUAUGAAAUUAUUAUAUUUUCUUUUAGAUCUAUGGUAGAAUUUGGAUUUAUAUUAGUGAAUUUUCAUAAUUUUAAGAUUUGUUGAACAAAGCAGAUUAGUACCUGGUUAGACAAAAAUUAAAAGAGCAGGAGUAAAGUUGUAUUUAAACUGAAAAGAUAUUGGCAGACAUUCUAAAUUAUCUUUGGAGGCUGAGUAGUAACUGAGAACCCUCAUUAACUACUUAAUUUUUUGACUCGUGUAUGAUCGUUUAUUUUAUUCUUAAGGAUUAUAAUAAAAAAUUUUUAAUUUAUUAAAAUAGAUAUAUACCCGGUUUAUGAUUUAAGAAACAUUUGGCCUACAAUAUUUUAUAUUAUGGAUUUUAGUUUUAGUUAACUAAAUGAAAUUGUAAAAGACAGUAAAAAAUUCUUAAUGUAUUUUUGAAGAUUAUCUAGAAGUGGUACAAAUCAUCCAUCAAUUGCCCAAAGGGGAGUAAGUUGUAGUAAAGUAGAUUUAGGGGAACCUGAAUCUAGUAAUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq new file mode 100644 index 0000000..9bb815f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.dugon.seq @@ -0,0 +1,2 @@ +>d.16.m.D.dugon +UAAAGGUUUGGUCCUGGCCUUCUUAUUGGUUCUUAGCGAGCUUACACAUGCAAGUAUCCGCGCGCCAGUGAGAAUGCCCUUUAAAUCACUCCCGAUCAUAAAGGAGCAGGUAUCAAGCACACACUCAUGUAGCUCAUAACGCCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGAUAGAAAUUUAGCCAUAAACGAAAGUUUGACUAAGCUACGCUAUAUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAAUUAAUAAGUACCGGCGUAGAGCGUGUUUAGGAGAAGACCCAUAAAUAAAGUUAAAUCAGAUCCAAGCCGUAGAAAGCUAAAGAUCAGACAAAAAUAAUCCACGAAAGUGACUUUAUCAGCUCUGAACACACGAUAGCUAAGACACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCGAUAGCUUCCAACAAAGCUACCCGCCAGAGAACUACUAGCAAAAGCUUAAAACUCAAAGGACUUGACGGUGCUUCACAUCCCCCUAGAGGAGCCUGUCCCAUAAUCGAUAAACCCCGAUAAACCUCACCCCCACUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCCAACCCUUAAAAGGUGCAAAAGUAAGCUCAAUGAUAGCCAUAAAAAAGUUAGGUCAAGGUGUAGCCCAUGUGGAGGUCUAAGAUGGGCUACAUUUUCUCUUAGAGAACAAUCAACCAACGGACGUCACUAUGAAACAAGUGACCAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAACUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAUUCAUAACCAUUCCACCAUAUAUGAUCCUAAUAGCAUAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUACU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq new file mode 100644 index 0000000..a39ca60 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.geoffroii.seq @@ -0,0 +1,2 @@ +>d.16.m.D.geoffroii +CAGAGGUUUGGUCCUGGCCUUACUGUUAAUUUUUAUUAGACCUACACAUGCAAGUUUCCGCAUCCCAGUGAGUAUGCCCUUUUAGCUUCACUGAAGUAUAAAGGAGCUGGUAUCAGGCACACUUAAUUAAGCAGCCCAUGACACCUUGUUUAACCACACCCCCACGGGUAACAGCAGUGACUAACAUUGAGCUAUAAACGAAAGUUUGACUAAAUCAUAAUAAAUAAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAACAGAAAAACGGCGUAAAGGGUGUUUAAGCAUAAACCUCAUAAAUAAAGUUAAAACUCAACUAUGCUGUAAUACGCCCUAGUUGGCAUUAAAAUAUACAACUUACGUGACUUUACUACUGCUGAAGACACUAAAGCUAAGGUACAAACUGGGAUUAGAGACCCCACUAUGCUUAGCCGUAAACCUAGGUAAUUAAAUAACAAAAUUACUCGCCAGAGAACUACUAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCCCUAGACCCUCCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCCCUUCUAGCUUAACAGUCUAUAUACCGCCAUCGUCAGCUCACCCCAAUAGGGCCCCAAAGUGAGCAAAAUCAUCUAAACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGCAAUGGGCUACAUUUUCUAUAUUAGAACAUAACGGAUUGUCUACUGAAAUAGAGGCAUGAAGGAGGAUUUAGUAGUAAAUUAAGAGUAGAGAGCUUAAUUGAAAUAGGCAAUAGGGUGCGUACACACCGCCCGUCACCCUCCUCGAUAAAGUAACCUUCAAUACCUAAUUAGAAUACGCUAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq new file mode 100644 index 0000000..e7d211c --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.novemcinctus.seq @@ -0,0 +1,2 @@ +>d.16.m.D.novemcinctus +CACAGGUCUGGUCCUAGCCUUACUAUUAAUUCAUAACAAAAUUACACAUGCAAGUAUCAGCACACCAGUGAGAAUGCCCUCUAACUCUUAUAGAUCAAAAGGAGCAAGCAUCAAGUACACACAGCCCUUACAGUAGCUCAUAACGCUUUGCUCAACCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCAAUAAGCGAAAGCUUGACUAAGUUAUGUUAUUAUAAGGGUUGGUAAAUUUCGUGCCAGCAACCGCGGUCAUACGAUUAACCCAAAUUAAUAGUUAUCGGCGUAAAGCGUGUUUAAGACACCUAGACAAUAGAGUUAAACCCUUACUACGCUGUAAAAAGCCUUAGUAGGACCAUAAACCCUUCAACGAAAGUGACUCUAAUUUAUCUGACUACACGAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACUAAAACAGUUCACAAACAAAACUGUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACAUCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAUACCUCACCACCCCUUGCUAAUACAGCCUAUAUACCGCCAUCUUCAGCAGACCCUAGUAAGGCACCACAGUGAGCACAAUAACAUACAUAAAGACGUUAGGUCAAGGUGUAGCUUAUGGGGUGGGAAGAAAUGGGCUACAUUUUCUAAUAAAGAGCAAAUACAAAAAACUUAAUGAAACAAUUUAAGACUAAGGUGGAUUUAGUAGUAAGCUAAAAAUAGAGAGUUUAGCUGAACCAGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCUUCAAUUAUAAGCGCCACAUAAACUAAAACACAUUAAUUCAGUAGCAACUAUAUAAGAAGAGACAAGUCGUAACAAGGUAAACAUACUGGAAAGUGUGUUUGGAUAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq new file mode 100644 index 0000000..5620601 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.D.virilis.seq @@ -0,0 +1,2 @@ +>d.16.m.D.virilis +AUAAAGUUUUAUUUUGGCUUAAAAGUUUGUUAUUAAUUUGAUUUAUAUGUAAAUUUUUGUGUGAAUAUUUAAUAAUUUAAAAAAUUAUUAAAUUUAUUAUAAUCGCAGUAAUUAAUUUUAUUAGUUAAAGAAAUUUAGAAAUAGCAAUAUUAAAGAGUAUAGAUUAAAUUGGUGCCAGCAAUCGCGGUUACACCAAUUAUACAAAUGAAUUUUUUUAGUAAAAGUUAAAUUGGUUUAAUUUAAAUAUAAUUAAAUUUAUUAAGUGAAAUUUUAAAUUUAAAAUUUUUAUUAAGUGAAUAAUUGAAACUUGAAAAUUUUAAAUAAAAACUAGGAUUAGAUACCCUAUUAUUUAAAAUGUAAAUAUAAAUACUUAAGUAGUAAUAGUUAAGUUCUUGAAACUUAAAAAAUUUGGCGGUAUUUUAGUCUAUCCAGAGGAACCUGUUUUGUAAUCGAUAAUCCACGAUGGACCUUACUUAAGUUUGUAAUCAGUUUAUAUACCGUCGUUAUCAGAAUAUUUUAUAAGAAUAUUAAUAUUCAAUAAUUUUUAUUAAAAUUUAUAUCAGAUCAAGGUGUAGCUUAUAUUUAAGUAAUAAUGGGUUACAAUAAAUUUAUUUAAACGGAUAAAAUUAUGAAAAAAUUUUUGAAGGUGGAUUUGGUAGUAAAAUUAUAAAGAUUAAUAAUUUGAUUUUAGCUCUAAAAUAUGUACACAUCGCCCGUCGCUCUUAUUAUUAAGGUAAGAUAAGUCGUAACAUAGUAGAUGUACUGGAAAGUGUAUCUAGAAUGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq new file mode 100644 index 0000000..52bb4a4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.E.rufescens.seq @@ -0,0 +1,2 @@ +>d.16.m.E.rufescens +CAAAGGUUUGGUCCUAGCCUUAUUAUUAGUUGUCAGUAAGAUUAUACAUGCAAGUAUCCGCCAACCAGUGAAAAUGCCCUCAUACUCGUCCACUACAAACGAUCCCAAAGGAGCCGAUAUCAAGCACACCCACGGUAGCUCAAGACAUCUUGCUCAGCCACACCCCCACGGGAUACAGCAGUAGUAAAAAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACUGAUUAGGGUUGGUCAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCAAAUUAAUGAUUAAACGGCGUAAAGUGUGGUUAAACACUUACCAAUGUAAAUAAAGUUAAACUAGCUCUCAGCUGUAAAAAGCUAAAGAUCUAUGGUAAAUAGACUAUUAAUGUAACUUUACUUAUAGUGAACCCACGAUAGCUAAGAUACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCGUAAACUUUGAUAAUUACUAACAAAAAUAUCCGCCAGAGAACUACAAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCCCUAGAGGAGCCUGUUGCAUAAUCGAUAAACCCCGAUAAACCCUACCAUCACUUGCUAAAUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAUAAGGAACAAUAGUAAGCUUAAACGCCCCCGCAAAAACGUUAGGUCAAGGUGUAACCUAUGUGAUGGAAAACAAUGGGCUACAUUUUCUACAUAAGAACACACGAACUCUUAUAUGAAAUUAUCAGAUAAAGGAGGAUUUAGAAGUAAGCCAGGAAUAGAGAGCCUGACUGAACUUGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUGUUUAAGACUAACAACCCUAUUACACUAAUACAAACAUAAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAGUAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq new file mode 100644 index 0000000..ec6581f --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.G.gorilla.seq @@ -0,0 +1,2 @@ +>d.16.m.G.gorilla +AAUAGGUUUGGUCCUAGCCUUUCUAUUAACUCUUAGUAGGAUUACACAUGCAAGCAUCCCCGCCCCAGUGAGUCACCCUCUAAAUCACCACGAUCAAAAGGAACAAGCAUCAAGUACGCAGAAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCCAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGCCAAUAGAAAUCGGCGUAAAGAGUGUUUUAGAUCAAUCCCCCAAUAAAGCUAAAAUUCACCUGAGUUGUAAAAAACUCCAGCUGAUAUAAAAUAAACUACGAAAGUGGCUUUAAUAUAUCUGAACACACAAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACUUCAACAGUUAAAUUAACAAGACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCACAUCCUUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACGAAGGCCACAAAGUAAGCACAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACUUCAGAAAACUACGAUAACCCUUAUGAAACCUAAGGGUAGAAGGUGGAUUUAGCAGUAAACUAAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUCUAUAUAGAGGAGAUAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq new file mode 100644 index 0000000..bb4f2d2 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.amphibius.seq @@ -0,0 +1,2 @@ +>d.16.m.H.amphibius +UACAGGUUUGGUCCCAGCCUUUCUGUUAAUUUUUAAUAGAAUUACACAUGCAAGUAUCCACACCCCAGUGAGAAUGCCCUCUAAAUCACCCAGAUCAAAAGGAGCGGGUAUCAAGCACACCAUACACCGUAGCUCAAAACGCCCUGCUCAGCCACACCCCCACGGGAAACAGCAGUGACCAAAAUUAAGCCAUGAACGAAAGUUUGACUAAGCCAUAUUAACCAGAGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACUCAAACUAACAGAAAUACGGCGUAAAGCGUGUUAAAGAAUUAAAAGUACAAAUAAAGUUAAAUUCUAACUAAACUGUAAAAAGCCCUAACUAGAAUAAAAAUCUACUACAAAAGUGACUUUAACAAUACUGACCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAGAUAAUUCCAAAAACAAAACUAUUCGCCAGAGUACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCAUACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUCCAGUCUAUAUACCGCCAUCUCCAGCAAACCCUAAAAAGGACUAAAAGUAAGCUCAACUAUUACACAUAAAGACGUUAGGUCAAGGUGUAACCUAUGGGCUGGGAAGAAAUGGGCUACAUUUUCUAGAACAAGAACACAACCCACCCGAACGAAAACUCCUAUGAAAGCUAGGAACUAAAGGAGGAUUUAGUAGUAAAUCAAGAGUAGAGUGCUUGAUUGAACAAGGCUAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAACACAAACCCAUAAACAUAAUAGCUAGACAAAACCAAAUGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq new file mode 100644 index 0000000..5a42913 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.auropunctatus.seq @@ -0,0 +1,2 @@ +>d.16.m.H.auropunctatus +CAAGGGUUUGGUCCUGGCCCUUCCAUUAGUUACUAAUAGGAUUACACAUGCAAGCCUCCGCAUCCCGGUGAAAAUGCCCUCUAAGUCAUAACUGACCUAAAGGAGCAGGUAUCAAGCACACAAAAUGUAGCUCAUAACGCCUUGCUCAGCCACACCCCCACGGGCUACAGCAGUGACAAAAAUUAAGCCAUGAAUGAAAGUUCGACUAAGCCAUAUUAAAUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUAACCCAGACUAAUAGACACACGGCGUAAAGCGUGUUCCAGAAACAACCUACCACUAAAGUUAAACCUUAACUAAGCCGUAAAAAGCCACAGUUAACAUGAAAAUACAACACGAAAGUAACUUUAAUACCCCAACUACACGACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAAUCUAGAUAGUUAACUUAACAAACCUAUCCGCCAGAGAACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACCUCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAAGGAAUAACAGUAAGCAAAAGUAUCUUAACAUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAGGUGGAAAGCAAUGGGCUACAUUUUCUACACAAGAACAUCUUACGAAAGUUUUUAUGAAAUCAAAAACUAAAGGAGGAUUUAGCAGUAAGCUGAGAAUAGAGCGCUCAGCUGAAUCGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUACACAAACCCAAACAUAACCUAUUAAAAUCACACUUAAUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUAAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq new file mode 100644 index 0000000..d10d756 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.2.seq @@ -0,0 +1,2 @@ +>d.16.m.H.lar.2 +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCCCCUGGCAAGAUUACACAUGCAAGCAUCCCCGCCCCGGUGAAAUCGCCCUUCAAAUCACCCGUGAUCAAAAGGAGCAGGUAUCAAGCACGCAGUAAUGCAGCUCAAAACACCCUGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUGCCAACCCAGGGUUGGUCAACUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCCAGUUAAUAGAGCCCGGCGUAAAGAGUGUUUUAGAUUGCUCCCUAAUAAAGCUAAGCUCCAUCCAAGUCGUAAAAAACUCUGGCUGCUAUAAAAUAAACUACGAAAGUGGCUUUAACACCUCUGAAUACACAAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACUUCAACAGUCAAAUCAACAAGACUGCUCGCCAGAACACUACGAGCAACAGCUUAAAAAUCAAAGGACCUGGCGGUGCUUCACACCCCCCUAGAGGAGCCUGUCCUAUAAUCGAUAAACCCCGUUCAACCUCACCAUCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACAAAGGCUAUAAAGUAAGCACAAACACCCACAUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGAUGGGAAGAGAUGGGCUACAUUUUCUAUGCCAGAAAACCACGAUAACCCUCAUGAAACUUGAGCGGUCGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGUGCUUAGUUGAACAAGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGCAUAUUUCAAGGAACCCCUAACUAAAUACUCCACGCAUCUAUGUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq new file mode 100644 index 0000000..88f8a65 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.lar.geno.seq @@ -0,0 +1,2 @@ +>d.16.m.H.lar.geno +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCCCCUGGCAAGAUUACACAUGCAAGCAUCCCCGCCCCGGUGAAAUCGCCCUUCAAAUCACCCGUGAUCAAAAGGAGCAGGUAUCAAGCACGCAGUAAUGCAGCUCAAAACACCCUGCCUAGCCACACCCCCACGGGAGACAGCAGUGAUAAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUGCCAACCCAGGGUUGGUCAACUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCCAGUUAAUAGAGCCCGGCGUAAAGAGUGUUUUAGAUUGCUCCCUAAUAAAGCUAAGCUCCAUCCAAGUCGUAAAAAACUCUGGCUGCUAUAAAAUAAACUACGAAAGUGGCUUUAACACCUCUGAAUACACAAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACUUCAACAGUCAAAUCAACAAGACUGCUCGCCAGAACACUACGAGCAACAGCUUAAAAAUCAAAGGACCUGGCGGUGCUUCACACCCCCCUAGAGGAGCCUGUCCUAUAAUCGAUAAACCCCGUUCAACCUCACCAUCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGACAAAGGCUAUAAAGUAAGCACAAACACCCACAUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGAUGGGAAGAGAUGGGCUACAUUUUCUAUGCCAGAAAACCACGAUAACCCUCAUGAAACUUGAGCGGUCGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGUGCUUAGUUGAACAAGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGCAUAUUUCAAGGAACCCCUAACUAAAUACUCCACGCAUCUAUGUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq new file mode 100644 index 0000000..6d7bbbc --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.moschatus.seq @@ -0,0 +1,2 @@ +>d.16.m.H.moschatus +CAUAGGUUUGGUCCUGGCCCUACUGUUAAUUGUAAUUAGACCUACACAUGCAAGCUUCCACAAUCCGGUGAGAUAUGCCCUACAGAUUACUUACCAUAAUCGUUAAGGAGCGGGCAUCAGGCACACCACAGGUAGCCCAUCACGCCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGACUAAUAUUAAGCCAUAAACGAAAGUUUGACUAAAUCAUAAUUAAAUCAGGGUUGGUAAAUUUCGUGCCAGCCGCCGCGGUCAUACGAUUAACCCAAGUUAACAGAAAACCGGCGUAAAGCGUGUUUAAGCACAAACCUACAAAUAAAGCUAAGACGCAACUAAGCUGUAAUACGCUAUAGUCAACAUUAAAAUACACUACAAAAGUGGCUUUAAUACCGCUGAAGACACGACAGCUAAGACACAAACUGGGAUUAGAUACCCCACUAUGCUCAGCUUUAAACCAAGAUAAUUAAACAACAAAAUUAUUCGCCAGAGAACUACUAGCAAUCGCUUAAAACUCAAAGGACUUGGCGGUGUCCUAAACCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCACGAUACACCUCACCCCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCUGGCCCCAACACGGGUAAUAAAGCAGCAAGAUUACUCAACCGUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGCAAUGGGCUACAUUUUCUAAAUUAGAACAAACGAAUUAUCUUAUGAAACCUAAGACAUAUGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAACAGGCAAUAGGACGCGCACACACCGCCCGUCACCCUCCUCGAUAAAACUGGAUAAAUAACUAAUAACUCCGAGCACAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGAACAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq new file mode 100644 index 0000000..790ca18 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.5.seq @@ -0,0 +1,2 @@ +>d.16.m.H.sapiens.5 +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGAACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAACCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACAGAAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUAAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq new file mode 100644 index 0000000..7292f31 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.H.sapiens.geno.seq @@ -0,0 +1,2 @@ +>d.16.m.H.sapiens.geno +AAUAGGUUUGGUCCUAGCCUUUCUAUUAGCUCUUAGUAAGAUUACACAUGCAAGCAUCCCCGUUCCAGUGAGUUCACCCUCUAAAUCACCACGAUCAAAAGGGACAAGCAUCAAGCACGCAGCAAUGCAGCUCAAAACGCUUAGCCUAGCCACACCCCCACGGGAAACAGCAGUGAUUAACCUUUAGCAAUAAACGAAAGUUUAACUAAGCUAUACUAACCCCAGGGUUGGUCAAUUUCGUGCCAGCCACCGCGGUCACACGAUUAACCCAAGUCAAUAGAAGCCGGCGUAAAGAGUGUUUUAGAUCACCCCCUCCCCAAUAAAGCUAAAACUCACCUGAGUUGUAAAAAACUCCAGUUGACACAAAAUAGACUACGAAAGUGGCUUUAACAUAUCUGAACACACAAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUCAACAGUUAAAUCAACAAAACUGCUCGCCAGAACACUACGAGCCACAGCUUAAAACUCAAAGGACCUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUCAACCUCACCACCUCUUGCUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUGAUGAAGGCUACAAAGUAAGCGCAAGUACCCACGUAAAGACGUUAGGUCAAGGUGUAGCCCAUGAGGUGGCAAGAAAUGGGCUACAUUUUCUACCCCAGAAAACUACGAUAGCCCUUAUGAAACUUAAGGGUCGAAGGUGGAUUUAGCAGUAAACUGAGAGUAGAGUGCUUAGUUGAACAGGGCCCUGAAGCGCGUACACACCGCCCGUCACCCUCCUCAAGUAUACUUCAAAGGACAUUUAACUAAAACCCCUACGCAUUUAUAUAGAGGAGACAAGUCGUAACAUGGUAAGUGUACUGGAAAGUGCACUUGGACGAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq new file mode 100644 index 0000000..dfde3d8 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.L.catta.seq @@ -0,0 +1,2 @@ +>d.16.m.L.catta +UAUAGGUUUGGUCCUGGCCUUACUAUUAGUUUACAGUAAGAUUACACAUGCAAGUAACCGCAUCCCAGUGAGAAUGCCCUCCAAAUCCCCUGAUUAAAAGGAGCAGGUAUCAAGCACACCAAUAGGUAGCUCACCACACCUUGCUAAACCACACCCCCACGGGAUACAGCAGUGAUUGAACUUAAGCAAUAAACGAAAGUUUGACUAAGCUAUACUGACACUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUAUUUCCCGGCGUAAAGUGUGUUUAAGAUUUAUAUAAAUAAAGUUAAUUUUUAUCCAAGCCGUAAAACGCCCCAGCUAAAACAAAACUAACCUACGAAAGUGACUUUAAUACUCUGAAGACACGACAACUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCGUAAACCUAAGUAAUUAACAAACAAAAUUACUCGCCAGAGCACUACAAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACUUCUUGCUAAUUCAACUUAUAUACCGCCAUCCCCAGCAAACCCUAUUAAGGCCCCAAAGUAAGCAAAAACACAUACAUAAAGACGUUAGGUCAAGGUGUAGUCAAUGAAGUGGAAAGAAAUGGGCUACAUUUUCUAAUAUUAGAACAACACCCCAACAGAAGCCUUUAUGAAACUAAAAGCCAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAUCACCAAUUAUUAAUUCACUAAUUCUACUAAACUCUAAACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq new file mode 100644 index 0000000..5f34aee --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.auratus.seq @@ -0,0 +1,2 @@ +>d.16.m.M.auratus +AAAAGGUUUGGUCCUAGCCUUAUAGUUAGUUAGAGGUAGAGUUACACAUGCAAAUCUCUAUAAACCAGUGUCAAAUCCCUAGGUUUUACUUUAAACCCUAAGGAGAGGGUAUCAAGCACAUACACAUAUAUAGCUAAAGACACCUUGCCUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAAAUUAAGCCAUAAACGAAAGUUUGACUUAGUCAUACCUCAUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAACUAUUCUCCGGCGUAAAAUGUGUUUUUAUUACGAACAUAAUAGAAUUAAAACCCAACUAAUAUGUGAAAAUUCAUUGUUGGACUUAAAAUCAAUAACGAAAGUAAUUCUAAUUAUAUUAAUACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUAAGUGAUUAAAUAACAAAAUCACUUGCCUGAGAACUACUGGCCACAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUAUACCUUACCACCCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCUUAAAAAAGAACAAGAGUAAGCAAGAGAAUACCCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUGGGCUGGGAAGUAAUGGGCUACAUUUUCUUCUAAAGAACAGUUACGCUAUCCUCUAUGAAACUUAGAGGACAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUACGUACACACCGCCCGUCACCCUCCUCAAAUUAAGCUAACUGUUAACUAUACCUAAUAUUGACUCAUAAACUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq new file mode 100644 index 0000000..1091d21 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.musculus.seq @@ -0,0 +1,2 @@ +>d.16.m.M.musculus +AAAGGUUUGGUCCUGGCCUUAUAAUUAAUUAGAGGUAAAAUUACACAUGCAAACCUCCAUAGACCGGUGUAAAAUCCCUUAAACAUUUACUUAAAAUUUAAGGAGAGGGUAUCAAGCACAUUAAAAUAGCUUAAGACACCUUGCCUUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAUAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACCUCUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUCUUCGGCGUAAAACGUGUCAACUAUAAAUAAAUAAAUAGAAUUAAAAUCCAACUUAUAUGUGAAAAUUCAUUGUUAGGACCUAAACUCAAUAACGAAAGUAAUUCUAGUCAUUUAUAAUACACGACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCAUAAACCUAAAUAAUUAAAUUUAACAAAACUAUUUGCCAGAGAACUACUAGCCAUAGCUUAAAACUCAAAGGACUUGGCGGUACUUUAUAUCCAUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGCUCUACCUCACCAUCUCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGUAUUAAAGUAAGCAAAAGAAUCAAACAUAAAAACGUUAGGUCAAGGUGUAGCCAAUGAAAUGGGAAGAAAUGGGCUACAUUUUCUUAUAAAAGAACAUUACUAUACCCUUUAUGAAACUAAAGGACUAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUUGAGCAAUGAAGUACGCACACACCGCCCGUCACCCUCCUCAAAUUAAAUUAAACUUAACAUAAUUAAUUUCUAGACAUCCGUUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq new file mode 100644 index 0000000..276037b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.M.putorius.seq @@ -0,0 +1,2 @@ +>d.16.m.M.putorius +CAAAGGUUUGGUCCUAGCCUUCCUAUUGAUUAUUAACAGAAUUACACAUGCAAGUCUCUACACCCCAGUGAGAAUGCCCUCCAAAUCUAUAUGUUGAUUAAAAGGAGCGGGUAUCAAGCACACUAAAUUAGUAGCUCAUAACGCCUUGCUCAACCACACCCCCACGGGAUACAGCAGUGAUAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGCCAUGUUAACAAAGAGCUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAGCCCGAAUCAAUAGGCAAACGGCGUAAAACGUGUUAAGGAUUAUAUUAUAUUAAAGUUAAAAUUUGACAAGGCUGUAAAAAGCUACUGUUAAUAUAAGAUAAACCACGAAAGUGACUUUAUUACUUCCAUCAACACGAUAGCUGAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUCAGCCCUAAACAUAAAUAAUUAUCACAACAAAAUUAUCUGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUACAUCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUCACCACUUCUAGCUUAAUCAGUCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAGGGAAGAAAAGUAAGCACAAUAAUAUUACAUAAAAAAGUUAGGUCAAGGUGUAACCUAUGAAGUGGGAAGAAAUGGGCUACAUUUUCUAACCAAGAACACACUCACGAAAGUUUUUAUGAAAACUAAAAACUAAAGGUGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCCUCAAGCAACACACUCAAAUACUACAUAAUAAAAGUAAACCUAAAGCAAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGGUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq new file mode 100644 index 0000000..c971496 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Manis.sp.seq @@ -0,0 +1,2 @@ +>d.16.m.Manis.sp +CAUAGGUUUGGUCCCAGCCUUUUUAUUAGUUUAUGAUAAAAUUACACAUGCAAGUAUCCGCCCUACGGUGAAAACGCCCUUUAGCCUUUACAAGUCAAAAGGAGCUGGUAUCAAGCACGCCAAUUUAAGGCAGCUAGUGACACCUUGCUUACGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAACCAUUAACGAAAGUUAGAUUUAGUUAUAUCAUUUAUGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCUAAUUAAUAAAAAACCGGCGUAAAAAGUGUCAAAGUGUAUUUAAAUCAAAUAAAAUUAAGCCCUAAUCAAGCUGUAAAAAGCCUCGAUUAUAGUAAAAAUAAACUAUGAAAAUAAUUUUAAUAAAACCCACACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCUUAAACCUAAAUAAUUAAUUAAACAAAAUUAUUCGCCAGAGUACUACUAGCAAUAGCUUGAAACUCAAAGGACUUGGCGGUGCUUCAUAUCCCUCUAGAGGAGCCUGUCCUAUAAACGAUAAACCCCGAUAAACCUCACCAAUCCUAGCUAAUGCAGCCUAUAUACCGCCAUCCUCAGCAAACCCUAAUAAAGGAACCAUAGUAAGCAAGAUCAUUGAAACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGAUUGGGAAGAGAUGGGCUACAUUUUCUAAAACAGAAUAAGACGAAUACCCUUAUGAAAAUAAGGGUUAAAGGAGGAUUUAGUAGUAAGACAAGAAUAGAGAGCUUGACUGAAUUAGGCCCUGAAGCACGCACACACCGCCCGUCACCCUCUUCAAAUUUCCAAAAAACAGUAAAUAUAUUAAUGAAUAACAAGAAUGAGAAGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAGGUGUGCUUGGAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq new file mode 100644 index 0000000..4a5338a --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.afer.seq @@ -0,0 +1,2 @@ +>d.16.m.O.afer +AUAAAGGUUUGGUCCUAGCCUUUCUAUUAGUUGACAGUAAAUUUAUACAUGCAAGUAUCUGCCUCCCAGUGAAAUAUGCCCUCUAAAUCCUUACCGGAUUAAAAGGAGCCGGUAUCAAGCUCACCUAGAGUAGCUCAUGACGCCUUGCUAAACCACGCCCCCACGGGAUACAGCAGUAAUAAAAAUUUAGCAAUGAACGAAAGUUUGACUAAGUUAUACUAUAACUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGUAAUACGGCGUAAAGCAUGAUUAGGGAAUAAUAUAAAUAAAGUUAAAUGUAAAUCAAAGCUGUAAAAAGCUCCUGAUUAACUUAAAAUAAAACACGAAAGUUACUUUACCACUCCUGAAUUCAUGAUAGCUAGGAUACAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCAUAAACUUAAAUAUUUCUCAACAAAAUUAUUCGCCAGAGAACUACAAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCAUCUAGAGGAGCCUGUUAUGUAAUCGAUAAACCCCGAUAUACCUCACCAUCACUUGCCAAUACAGCCUAUAUACCGCCAUCUUCAGCAAACCCUUACAAGGAAUAAUAGUAAGCCAAAUUAUUACCAUAAAAACGUUAGGUCAAGGUGUAGCCAAUGUGAUGGCAAUAAAUGGGCUACAUUUUCUAUUUUAAGAACAUAUCCCUACGAAAACCCAAAUGAAACCAAGGCUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAACUACUAGUAUUACUAAAAAUAUUUCACUACAUAAACGUACUAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq new file mode 100644 index 0000000..fb058b0 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.anatinus.seq @@ -0,0 +1,2 @@ +>d.16.m.O.anatinus +UAAAGGUUUGGUCCUAGCCUUACUGUUAGAUUUGAUUAGAUUUAUACAUGCAAGUAUCCGCAACCCAGUGAGAAUACCCUAAAAACUCUUAACAAGUUAGAAGGAGUAGAUAUCAGGCACACUAAAGUAGCCCACAACAUCUUGCCCUAGCCACACCCCCACGGGACACAGCAGUAAUAGAAAUUAGUCAAUAAACGCAAGUUUGAACAAGUCAUAAUCAAUAAGAGUCGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUGACUCAACCUAACAAAUAACGGUGUAAAACGUGUUUAAAAACUUAAACUAAUAAGAUUAAAGUAGAACUAAACUGUGAUAAGUCAUAGUUAAUACUAAAGCCAUCUACGAAAGUGAUCUUAGACUAAUUGAAUACACGAUAGCUAAGGUACAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUCAAGUCGUUUAAUAACAAAACUACUCACCAGAGAACUACUAGCAACAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCAUCUUUUGCCACUACUGUCUAUAUACCGCCAUCGUCAGCCAACCCUAAAAAGGAACAAAAGUAGGCGUAAUCAUUUUUCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUAAGAUGGAAGAAAUGGGCUACAUUUUCUACAUUAGAACAUACGAAAAACUCUAUGAAACUAGAGUAUUAAGGAGGAUUUAGUAGUAAGCCAAGAAUAGAGAGCUUGACUGAACUGGGCAAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAUCAAGCAACACAAACAUUCCUAAAAUCCCAACGCUUUUCAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACCGGAAGGUGUGCUUGGAAUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq new file mode 100644 index 0000000..d11a7f6 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.aries.seq @@ -0,0 +1,2 @@ +>d.16.m.O.aries +UAUAGGUUUGGUCCCAGCCUUCCUGUUAACUUUCAAUAGACUUAUACAUGCAAGCAUCCACGCCCCGGUGAGUAACGCCCUUCGAAUCACACAGGACUAAAAGGAGCAGGUAUCAAGCACACACUCUUGUAGCUCACAACGCCUUGCUUAACCACACCCCCACGGGAGACAGCAGUAACAAAAAUUAAGCCAUAAACGAAAGUUUGACUAAGUCAUAUUGACCAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUGACCCAAGCUAACAGGAGUACGGCGUAAAGCGUGUUAAAGCAUCAUACUAAAUAGAGUUAAAUUUUAAUUAAACUGUAAAAAGCCAUAAUUAUAACAAAAAUAAAUGACGAAAGUAACCCUACAAUAGCUGAUACACCAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACACAAAUAAUUAUAAAAACAAAAUUAUUCGCCAGAGUACUACCGCAACAGCCCGAAACUCAAAGGACUUGGCGGUGCUUUAUACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCAAUCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAAGGGACAAAAGUAAGCUCAAUAAUAACACAUAAAGACGUUAGGUCAAGGUGUAACCUAUGGAGUGGGAAGAAAUGGGCUACAUUUUCUACCCAAGAAAAUUUAAUACGAAAGCCAUUAUGAAAUUAAUAGCCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUCAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUAAAUAUGAUAUACUUAAACCUAUUUACAUAUAUCAACCACACGAGAGGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq new file mode 100644 index 0000000..018a895 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.cuniculus.seq @@ -0,0 +1,2 @@ +>d.16.m.O.cuniculus +UAAAGGUUUGGUCCUGGCCUUUUUAUUGUUUUGUAGCAACCUUACACAUGCAAGACUCCUCACGCCAGUGAGAAUGCCCUUAACAUCAAACUAGAUCAAGAGGAGCGGACAUUAAGCACACUAAUCAGUAGCUCAAGAUGCCUUGCUUAACCACACCCCCAAGGGAUACAGCAGUGAUAAAUAUUUAGCAAUGAACGUAAGUUUGACUAAGUUAUGCUACUUUAGGGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAAAUAUCCGGCGUAAAGCGUGAUUAGAAUAAACAACAAAAUAAAAUCAAAUAACAACUAAGCUGUAGAAAGUAAUAGUUGCAAACAAAAAUAAACAACGAAAGUGAUUUUAUACUCUUCGAACUCACGAUAGCUAAGGCCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUUUGAUAAUUUCAUAACAAAAUUAUUCGCCAGAGAACUACAAGCCAAAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCACCUAGAGGAGCCUGUUCCGUAAUCGAUAAACCCCGAUAAACCCUACCACUCUUUGCCAACUCAGCCUAUAUACCGCCAUCUUCAGCGAACCCUAAAAAGGAGCAAAAGUAAGCUCAAUUACCACCGUAAAAACGUUAGGUCAAGGUGUAGCCCAUAGAGUGGAGAGCAAUGGGCUACAUUUUCUACUUCAGAAUAUACGAAAGCCCUUAUGAAACUCUAAGGGCCAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGUGCUUAAUUGAACAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUGACAAAUAUUUACUUAUACCUAAUUACAUAAAUAGACAAGCAUAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGACAUUU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq new file mode 100644 index 0000000..bfc3821 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.O.virginianus.seq @@ -0,0 +1,2 @@ +>d.16.m.O.virginianus +CAGAGGUUUGGUCCCAGCCUUCCUAUUAAUCCCUAGCAGACUUACACAUGCAAGUAUCCUCAUCCCAGUGAAAAUGCCCUCCAAGUCAAUAAAACUAAGAGGAGCUGGUAUCAAGCUCACACCCGUAGCUCAUGACGCCUUGCUCAGCCACACCCCCACGGGAGACAGCAGUGAUAAAAAUUAAGCUAUAAACGAAAGUUUGACUAAGUCAUGCUAAUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAGUUAAUAGGCACACGGCGUAAAGCGUGUUUAAGCACUAUGCCAAAUAGAGUUAAACUCCAAUUAAGCUGUAAAAAGCCAUAAUCAAGACGAAAAUAAAUAACGAAAGUAACUUUACAACCGCUGAAACACGAUAGCUAAGAUCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAGUUAUAUAAACAAAACUAUUCGCCAGAGUACUACCGGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCUUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUUACCACCCCUUGCUAAUACAGUCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAACAAAAGUAAGCACAAUCAUUAUACAUAAAAACGUUAGGUCAAGGUGUAACCUAUGGAGUGGAAAGAAAUGGGCUACAUUUUCUAAUCUAAGAAAACUCUUUACGAAAGUUACUAUGAAAUUAGUAACCAAAGGAGGAUUUAGCAGUAAACUAAGAAUAGAGUGCUUAGUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCUUCAAAUAGGCACAAUACACUUAAAUUUAAUUAUACGUAUUAAUCAUAUGAGAAGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq new file mode 100644 index 0000000..d59ad6b --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.cinereus.seq @@ -0,0 +1,2 @@ +>d.16.m.P.cinereus +UAAAGGUUUGAUCCUAGCCUUACUGUUAGUUUUAAUUAAACUUACACAUGCAAGUUUCCGCAACCCAGUGAGAAUGCCCCCAAAAUUUAUACACAAUUUAGCAGGAGCAGACAUCAGGUUCACUACAAAGUAGCCCAUAACGUCUUGUCCAACCACACCCCCACGGGAUACAGCAGUGAUUAACAUUAAGCUAUAAACGAAAGUUUGACUAAAUUAUAAUUAUCUAGGGCCGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUGACCCAAACUAACAGAUGUCGGCGUAAAGCGUGUACAAUCCAACAACCAAAAUAAGGCUAAAACUCAAUCAUGCUGUAAUACGCUAUAGCUAACAUUAAAAAAUGCAACCAAAGUGGCCUUAAUACUGACCAAAACACGACAGCUAAGACUCAAACUGGGAUUAGAUACCCCAUUAUGCUUUAGCGUAAACUUAGAUAGUUUAAUAACGAAACUAUUCGCCAGAGAACUACUAGCCAGCGCUUAAAACUCAAAGGACUUGACGGUGUCCUAAGCCCAUCUAGAGGAGCCUGUCCUAUAACCGAUGAACCCCGAUACACCCCACCUCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCCUACCCCAAUAGGGACCAAAAGUAAGCAAAAUCAUCAACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGAGGAAAGUGAUGGGCUACAUUUUCUAACAUAGAAAAUUACGGACUAUCUUAUGAAACCUAAGAUAUACGAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAACAGGCAAUAGGACGCGUACACACCGCCCGUCACUCUCUUCAACAUAAACAAACCAAAUAACUAAUAAAAUAAAUAAAUAAAGAAGAGAAAAGUCGUAACAUGGUAAGUGUACCGGAAGGUGCACUUGGAUCAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq new file mode 100644 index 0000000..f347a38 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.P.polycephalum.seq @@ -0,0 +1,2 @@ +>d.16.m.P.polycephalum +GUUUUAAUAUAAUAAUGAGUUUGAUCCUGGCUCCGAGAGAAUGCUAGCAACUUACUUGAUACAUGCUAGUCGAACGCUUAUAUGAGCGUGGCGUACGAGCGACAAGGGCAAAGAUAGAAAAUACAUCAGUCAAGGGAAAUCCUAGAUUUAAAAGAUUAUAUCGCUGAAUGUAAGGUCUUUGUGAGAUUAGGUUGUUGGUAAGAUAAAAGCCUACCAAGCCGAUGAUCUCUAGCUGGUCUGAGAGGAUGUACAGCCGCGUCGGAAAUGCAAUAAGGUCCGGACUCCCUCGGGAGGCUGCAGUAGGGAAUCGUGAACAAUGUGCUAACGCUUGAUUCUAUAAUGUUGCGUGGGGGAUACAAAAAACAUUAUUUUAUACUUAUUGUUUUAUAAACAAAUUUAUAUAUAAAAUAGUGAUAAUUCUAGCAACGACUUAAGCGCAAUAAAAGUUUCCGUAAAAAGAGAUUUUUAUCUGUGUCUUCUGUAGCGUGCCUUUCUAGUAGACGGCAAGUUGUCUUAAACCCCUUUUUUUACGAUUAUAAUGACUGUAGUUAGUAUAUAUCUAUUUAUCAAGAUGAGGGUUGGUAAAUUACAUUUUGUUUGUUAGACUAAAAUACUCGAGCAAAAAUGCCUUAUGCUGCUUUGCUUAAAAAUAUCAAACCCCGGCUAACUUCGUGCCAGCAGCCGCGGUAAAACGGGGGGGGUUAGUGUUAUUCGUGAUGACUGGGCGUAAAGGGUACGUAGGCAGAUAAUUGAAAAUACAGUAAAAAACUGAGGUAAACCCUCUUCAUUCUGUAUUCACUCAUUAUCUUGAGUUCAGAAGGCGGUUUAUUGAAUUCUCGAAGGAAGGGUGAAAUCUGUUGAUAUCUGGAAGACAUUCGAUAGCGAAAGCAACAUCCGAUUCUGAUCUAACGCUCAGGUACUAAAGUAUGGGGAUCAAAUAGGAUUAGAGACCCUAGUAGUCCAUACCUUAAACAAUGAGUGUUCAACGUCUUUAAUAUAGUCAAUAUAUUUAGGGGGUUUAAAGCUAACGCGUGAAACACUCCGCCUGGGGAAUGUGGCCGCAAGGUCUAAACUCAAAGGAAUUGACGGUGACUUAUACAAGGGGUGGAGCAUGUGGUUUAAUUCGACAUACCGCGCAAAACCUUACCAAUUUUUGUAUCUGGUUUCUUUUCGUUAGCCAUUUAUUUGGUUAGCCUUCUUCUUUCUGUUGAAGGUCUACUACGAUAUCGAUUGAAGAUGUGGGUGUUUCUAUGCGUAAGCAUGAUCUAGCUAUUUUCAAUUAACGGUAACCAAUGACAAGAGCUGCAUGAUUGUCGUAAGUUCGUGCCGUGAGGUGUUGGGUUCAUUCCAUAAACGAACGCAACCCUUUUGAUUAGUUGCAUAAUGGAUGAAAGUUUAAACUGGAUAUCCAUGUUCACUAGUUCAACCAGCCCUUCUACCUUUAGGGAUUAAGGACAGGUCCACGUCAAAUCAUUAUGGCCUUAAUAGAUUGGGCUACACAUGUGCUACAUUGAUGAUCGACAACAAGAAGCAAUGGCGUGAGCCUGAGCAAAUCUUUAAAAGACAUUUCAGUCCGAAUUGUUCUUUGAAACUCAAGAGCAUGAAGCCGGAAUCUCUUGUAAUCGUGGAUCAUUACGCCACGGUGAAUUAGUACAAAAGUCACGUACAGACCGCCCGUCAUGCUAUGGAAACUAUUUGAAGUAGAAGUUACAAGGUUUCAAUUGUUUCGAUAGACCACCUUAUUGAAAGUUUUCAUAAGGCCUUGACAUUCUGUUGGCUUUGUACACGACUCUUUAUUUAGGGACUGGAGUAAAGUCGAAACAGGGUAGUGGUAGAAGAAUCUGCUGCUGGACCAUUAUUA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq new file mode 100644 index 0000000..a016faf --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.norvegicus.seq @@ -0,0 +1,2 @@ +>d.16.m.R.norvegicus +AAAGGUUUGGUCCUGGCCUUAUAAUUAAUUGGAGGUAAGAUUACACAUGCAAACAUCCAUAAACCGGUGUAAAAUCCCUUAAAGAUUUGCCUAAAACUUAAGGAGAGGGCAUCAAGCACAUAAUAUAGCUCAAGACGCCUUGCCUAGCCACACCCCCACGGGACUCAGCAGUGAUAAAUAUUAAGCAAUGAACGAAAGUUUGACUAAGCUAGUACCUCUCAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAAUUAUUUUCGGCGUAAAACGUGCCAACUAUAAAUCUCAUAAUAGAAUUAAAAUCCAACUUAUAUGUGAAAAUUCAUUGUUAGGACCUAAGCCCAAUAACGAAAGUAAUUCUAAUCAUUUAUAUAAUGCACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACCUUAAUAAUUAAACCUACAAAAUUAUUUGCCAGAGAACUACUAGCUACAGCUUAAAACACAAAGGACUUGGCGGUACUUUAUAUCCGUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUCUACCUUACCCCUUCUCGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGCACUAAGUUAGCACAAGACAACAUAAAACGUUAGGUCAAGGUGUAGCCAAUGAAGCGGAAAGAAAUGGGCUACAUUUUCUUUUCCCAGAGAACAUUACGAAACCCUUAUGAAACUAAAGGACAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAUAGAGCAAUGAAGUACGCACACACCGCCCGUCACCCUCCUCAAAUUAGAUUGACAUUCACAUAUACAUAAUUUCACUAACAAAUUUAUGAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq new file mode 100644 index 0000000..1a6dfd1 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.R.unicornis.seq @@ -0,0 +1,2 @@ +>d.16.m.R.unicornis +CAUAGGUUUGGUCCUAGCCUUUCUAUUAACUAUUAGUAAAAUUACACAUGCAAGUAUCCGCACUCCAGUGAGAAUGCCCUCUAAAUCACCCAUAACGAUUAAAAGGAGCAGGUAUCAAGUACACUAAUAACAGUAGCUAACAACACCUUGCUCAACCACACCCCCACGGGAGACAGCAGUGACAAAAAUUAAGCAAUAAACGAAAGUUUGACUAAGUUAUACUAAGCAGAGCCGGUAAAUUUCGUGCCAGCCACCGCGGCCAUACGAUUGACUCAAAUUAAUAGAACCUCGGCGUAAAGCGUGUCAAAGAUAUAACCCCUAAUAAAGUUAAAAACAUAGUUAAGCUGUAAAAAGCUAUAACCAAGAUAAAAUAAACCACGAAAGUGACUUUAAUAUAUCACCCACACUACAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCCAAACUCAAAUAAUUCUUCCCAACAAAAUUAUUCGCCAGAGUACUACUAGCAACAGCCUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCCCUAGAGGAGCCUGUUCCAUAACCGAUAAACCCCGAUAAACCUUACCAGCCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCCAACCCUAAAAAGGAACCAAAGUAAGCACAAGUAUAAGACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGAUGGAGAGAAAUGGGCUACAUUUUCUACUUCAAGAACAACAACUACCCAAACGAAGGCUUUUAUGAAAUUAAAAGCUAAAGGAGGAUUUAGCAGUAAAUUAAGAAUAGAGAGCUUAAUUGAACCAGGCCAUAAAGCACGCACACACCGCCCGUCACCCUCCUUAAAUAUCAUAAACCACAACACAACAUAUUAACGUACGUUGAACAUAUAAAAGGAGACAAGUCGUAACAAGGUAAGUGUACUGGAAAGUGCGCUUGGAUAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq new file mode 100644 index 0000000..ec9dd34 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aestuans.seq @@ -0,0 +1,2 @@ +>d.16.m.S.aestuans +UAUAGGUUUGGUCCUAGCCUUUUUAUUAAUUCUUAGUAGACUUACACAUGCAAGUAUCCCCGCCCCAGUGAGAAUGCCCUCUAUCUCCAUAAGGAUCUAAAGGUGCAGGUAUCAAGUACGCUCUCUCGAGCAGCUCAUGACACCUUGCUACACCACACCCCCACGGGACACAGCAGUGAUUAAAAUUGAGACAUAAACGAAAGUUUGACUGAGUUAUACUAAUAAUUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCUAGUUAAUAAAACACGGCGUAAAGCGUGAUUAAGGAAUAACCCCAAAUAAGAUUAAGCUCUGACUAAGCUGUAAAAAGCCUUAGUUAAAAUAAAAAUUUAUAAACGAAAGUAAUCUUACAACCCCUGAAUUCACGAUAGCUAAGGCCCAAACCGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUACUCAAAUAACAAGAGUAUUCGCCAGAGAACUACUAGCCACUGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUACCCCUCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGUUAAACCUCACCACUCUUUGCAAUGUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAUAAGGUAUCGCAGUAAGCACAAGAAUUCUGCAUAAAAACGUUAGGUCAAGGUGUAGCCUAUAGAGUGGGAAGAAAUGGGCUACAUUUUCUAAUUUCUUUAGAACAUUUCACGAUAGCUGUCAUGAAACAUGAUCAGCCCAAGGAGGAUUUAGUAGUAAGUUGGGAAUAGAGUGCCCAACUGAAUUGGGCAAUAAAGCACGCACACACCGCCCGUCACCCUCUUCAAGCAUCCAUGAUAACCCAUAUAAAUAAUACAAAAAUCUCCUAAUGCAAGAAGAGACAAGUCGUAACAAGGUAAACAUACUGGAAAGUGUGUUUGGAAUAUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq new file mode 100644 index 0000000..e30ce56 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.aquaticus.seq @@ -0,0 +1,2 @@ +>d.16.m.S.aquaticus +UAAAAGGUUUGGUCCUGGCCUUUCUAUUAGCUGUCAGUAAAAUUACACAUGCAAGUAUCCGCGCCCCAGUGAAAAUGCCCUUGAAGUCAUCAUAGACAUAAAGGAGCCGGCAUCAAGUACACCAUAAUGGUAGCUAACGACGCCUUGCUUAGCCACGCCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCUAUGAACGAAAGUUUGACUAAGUUAUACUGAUAUAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAAUAACCCAAGUUAAUAGAUACACGGCGUAAAGAGUGUUAAAGAACCUGGCAUUGUAAAUAAAGCUAAGACUUAACUAAGACGUAAAAAUCUCCAGUUAAAGUAAAAACAAACUACGAAAGUGGCUUUAUAUUAUUCUGAUCACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACUAAGACAAUCCAACUAACAAGAUUGUUCGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUUAUAUCCCUCUAGAGGAGCCUGUUCUGUAAUCGAUAAACCCCGAUAAACCUCACCAACCCUUGCUAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUUAAAGGGAGCCACAGUAAGCACAAGUAUAUACAUAAAAACGUUAGGUCAAGGUGUAGCUAAUGAGUUGGGAAGAAAUGGGCUACAUUUUCUAUAUCUAGAACACUUUAACGAAAGUCUUUAUGAAACGAAAGACUAAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGUGCUUAAUUGAAUUAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGUACUAAAGCCAGUCAAUAUACAUAAUAUAUAGGCAAUAAAUACAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUAAC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq new file mode 100644 index 0000000..af65bac --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.scrofa.seq @@ -0,0 +1,2 @@ +>d.16.m.S.scrofa +CACAGGUUUGGUCCUGGCCUUUCUAUUAAUUCUUAAUAAAAUUACACAUGCAAGUAUCCGCGCCCCGGUGAGAAUGCCCUCCAGAUCUUAAAGAUCAAAAGGAGCAGGUAUCAAGCACACCUAUAACGGUAGCUCAUAACGCCUUGCUCAACCACACCCCCACGGGAAACAGCAGUGAUAAAAAUUAAGCCAUGAACGAAAGUUUGACUAAGUUAUAUUAAUUAGAGUUGGUAAAUCUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAAUUAAUAGAUCCACGGCGUAAAGAGUGUUUAAGAAAAAAAAAUCACAAUAGAGUUAAAUUAUAACUAAGCUGUAAAAAGCCCUAGUUAAAAUAAAAUAACCCACGAAAGUGACUCUAAUAAUCCUGACACACGAUAGCUAGGACCCAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCCUAAACCCAAAUAGUUACAUAACAAAACUAUUCGCCAGAGUACUACUCGCAACUGCCUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAGACCUUACCAACCCUUGCCAAUUCAGCCUAUAUACCGCCAUCUUCAGCAAACCCUAAAAAGGAACAAUAGUAAGCACAAUCAUAGCACAUAAAAACGUUAGGUCAAGGUGUAGCUUAUGGGUUGGAAAGAAAUGGGCUACAUUUUCUACAUAAGAAUAUCCACCACACGAAAGUUUUUAUGAAACUAAAAACCAAAGGAGGAUUUAGCAGUAAAUCAAGAAUAGAGUGCUUGAUUGAAUAAGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAGCAUGUAGUAAUAAAAAUAACCUAUAUUCAAUUACACAACCAUGCAAGAAGAGACAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUUACC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq new file mode 100644 index 0000000..5a2d1d3 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.S.sinuspaulianus.seq @@ -0,0 +1,2 @@ +>d.16.m.S.sinuspaulianus +AAAAGAAAGAAUUUAAUUUUGGUUCCGAUUGAACGUUUUUCAGUAGUUUUAAGACAUGCAAAUCGUUAUUUCUGAAAGUAAAUUUUUAUUUAAAAUUAUAUAAAUAAUAACUAAAUAAAAAUGAUAAUAUGAAAUAAGGUGUAGAGGUGAGGAUAGUAAAUAAGAUACCCUGUAGUCUUCAUAGAUAGAAGAUAUUAUUCUAAGUAAAUUUUUUAAAUUUAUUACUAGUAUUUUUAAAUUAAUUUGCUUGCAUUAUAUAAAAUUAUAAUUGUUUUUCAUUAAUUGCAAAAAUUUAAAUAAAAAUGACUAAAGCAAAAAAAUUAUUUAAAUAACAAUAAUGUAAAAUAAAUGAAUAAAAUAAAAAAGCUAUUUUUAUUAAAAAAAGGAAAUUUUCUGCUAUAGGAUUCUAUUUAUUUUGAUUAGGUAGUUGGUAUGGGUAAAGGCCUACCAAGCCGACAAUCAAUAGCCAUGCUUGACAGAGCAGAUGGCCACAUUGGGAAUGAAAUCUCCCAAGUAGUUUUAUACUACCAGCAGUCAAGAAUAUUAGUCAAUGCUCGUAAGAGUGAACUAGCUAACUGAAAUCGCAAAUGUGUCAUUUGUGAUAAAGUAAGAGAAAAUUAUGAUAUUAUCUUACUACUAGUGCUGUCCAAAACUGGUGCCAGAAGACUCGGUAAGGCCAGAGGCGCAAACGUUAGUCGUCCUAAUCAGGCGUAAAGGGUUUGUAGGCUGCUUUGAAAGUCUUAUUAUUAUAAUAGCUAUUAAAUGAUAAGAUGAAUUGAAGCUAGAAUCUAAUAGAGGGUAAAACAAAUAAUAUUUAAAGUAAGGAUUAAAUCUCAAGAGUUUAGAUGGAAUACUAACGGUUAAAGCUUUUAUCUAUCUACAGAUUGACGCUGAGAAACGAAAGGGAGGUAAGGAAACAGGAUUAGAUACCCAACUACUGCUCCCUGUCAACGAUGAAUGGUGGUUGCUAGUUAUAACUACUUUAAGUAAAUAUUUUAUAUUAUAUAAGAUAAAAUAAGUAGUUAAAAUGACUGGUAGCGAUGCUAACGCGUUAACCAUUCCGCCUUGUGAGUACGACUGCAAAGUUGAAAACAAAAAAAUUAGUCGGUUUCGAAGCAAACGAAGUGAAGCAUGUUAUUUAAUACGAUAAUCCGCGUAAAAUCUUACCAGUUCUUGCAUACAAACUUUUUUUAUAAUAAUUUAAAUUAAAUUUUAAAUAGUUAUUUAAAAAGGAGUGUUUUUACUUUUUUAAAAAUACUUAGAUACAGGUGUUGCAUGGCUGUCGUCAGUCCGUGCUGUGAGAAGUUUGGUUAAAUCCGCUAACGGACAAAAUCCCUGUUGUUAAUUUAUACUUAACAAUUAAUGAUACUGAUAGAGCAUCAUUUGGGGCGAAGACAAGUCGUUAUGGCCCUCAUGAACUGGGCUAUAGACGUGCCACAAAGACUUUAACAAAGUGAAGCGAUACUGUUCCCUUAAUAUUUUUCUAAAGAAUUUUAUUAGAUUUAAUUAUAACAAUUAAAUUAUAGGGAAUUUAAGGAGGAGCUAAUCAUUAAAAAAAGUCAAACUAUUAAAUAUAGUCGGAUUGUCAUCUGAAACUCGGGGACAUGAAGAAGGAAUUUCGAGUAAUCGUUGAUCACUACGCAACGGUGAAGCUAGCAUUCGGAAUGAACUAACCGUCUGUCGCUGGGAAGGAGCUUAACUUGGUGGAAACUGGAAUGAAGUUUUAACUUUUACAAAAAUUAAAUUUUUAUUUAGUAUCUUUGAUAUUUUAUUUUUAAUUUAUUAGUUUUUUUUUCGUUAGAUUUUUUUUAAUUUAUUGCUUAAUUAAAAAGUAUUAUUUUUGUUUAAAGAAUAAAUACUUGUCUAACAAUGUUAAAUUUAAAACGAUUUUGUUAAGCAAAUUAGCUCUAGUUAAACCAAUUAAGUAACAUCUCAAAAGUCAUAGCAAGGUAGCCGUACUGGAAAGUGCUGCUGUAAAAUAAAACGA diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq new file mode 100644 index 0000000..e00de33 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.V.ursinus.seq @@ -0,0 +1,2 @@ +>d.16.m.V.ursinus +CAAAGGUUUGGUCCUAGCCUUACUGUUAAUUUUAAUUAAGCCUACACAUGCAAGUUUCCGCUGCCCAGUGAGAAUGCCCUCAAAAUUCUACAAUCGAAUCAACAGGAGCAGGUAUCAGGCACACCCAUCCCGGUAGCCCAUAACACCUUGCUUAGCCACACCCCCACGGGAUACAGCAGUGACUAACUUUAAGAUAUGAACGAAAGUUUGACUAAAUUAUAAUUAUACAGGGUUGGUAAAUUUCGUGCCAGCCGCCGCGGUCAUACGAUUAACCCAAAUUAACAGAACACCGGCGUAAAGCGUGUUUAAGCGCAAAUCUCAAAAUAAAGUUAAUACUUAACUAAACUGUAAUACGCCCUAGUUAACAUUAAAAUAAACAACUAAAGUGACUUUAAUUUCGCUGAAUACACGACAACUAAGACUCAAACUGGGAUUAGAUACCCCACUAUGCUUAGUCAUAAACCUAGGUAAUCCGAUAACAAAAUUAUUCGCCAGAGAACUACUAGCCACCGCUUAAAACUCAAAGGACUUGGCGGUGCUCUAAACCCACCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUACACCUCACCCCUUCUUGCCAAUACAGCCUAUAUACCGCCAUCGUCAGCUCACCCCAAUAGGGAACAAAAGUGGGCAAAAUCAUUCACCAUAAAAACGUUAGGUCAAGGUGUAGCAUAUGAAGGGGGAAGUAAUGGGCUACAUUUUCUAAAUUAGAAAACCAACGAACUAUCUCAUGAAACCCUGAGUCAUACGAAGGAGGAUUUAGUAGUAAAUUAAGAAUAGAGAGCUUAAUUGAAAUAGGCAAUAGAGCGCGCACACACCGCCCGUCACCCUCCUCAACACAAACCGUCACAUUAACUAAUAAGUUAUCCAAAAAAAGAGGAGAAAAGUCGUAACAUGGUAAGUGUACUGGAAGGUGCACUUGGAGUAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq new file mode 100644 index 0000000..dc25fe7 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.X.laevis.seq @@ -0,0 +1,2 @@ +>d.16.m.X.laevis +UAAAGGUUUGGUCCUAGCCUUAUUAUCAACUUUUUCUGAACUUACACAUGCAAGCAUCCGCACUCCCGUGAAAAUGCCCUUAAGCCUCUUAAACAGGGGAUAAGGAGCCGGUAUCAGGCACAACUAAUAGCCCAUGACACCUUGCUCUGCCACACCCACAAGGGAAUUCAGCAGUGAUAAACAUUGAACAUGAGCGACACAAAGCUCGAUUCAGUUACAGUAAAUAGAGUUGGUCAAUCUCGUGCCAGCCGCCGCGGUUAUACGAGAAACUCAAGUUGAUCAUUUUCGGCGUAAAGCGUGAUUAAAGUAACCCAAACUAGAGUCAAACUCCAACCAAGCUGUCGCCGCUUUCGUUGGUUUGAAGAACACUCACGAAAGUAACUCUACCCAUAUUACACUUGAACUCACGACCGCUAGGAAACAAACUGGGAUUAGAUACCCCACUAUGCCUAGCCAUAAACUUUGACUACUUACGCAAAAAUCCGCCAGAACUACGAGCCUAAGCUUAAAACCCAAAGGACUUGGCGGUGCUCCAAACCCACCUAGAGGAGCCUGUUCUGUAAUCGAUACCCCUCGCUAAACCUCACCACUUCUUGCCAAACCCGCCUAUAUACCACCGUCGCCAGCCCACCUCGUGAGAGAUUCUUAGUAGGCUUAAUGAUUUUUCAUCAACACGUCAGGUCAAGGUGUAGCAUAUGAAGUGGGAAGAAAUGGGCUACAUUUUCUAUACCUUAGAAUAAACGCAAGAUCUCUAUGAAACCAGAUCGGAAGGCGGAUUUAGCAGUAAAGAGAAACAAGAGAGUUCUCUUUAAAACGGCCCUGGAGCGCGCACACACCGCCCGUCACCCUCUUCUACAAAAAUCAACCAAUUUUAUAAACACACAAUUAACACAAAGAAGAGGCAAGUCGUAACAUGGUAAGCACACCGGAAGGUGUGCUUGGAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq new file mode 100644 index 0000000..47e7bd4 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.californianus.seq @@ -0,0 +1,2 @@ +>d.16.m.Z.californianus +CAAAGGUUUGGUCCUAGCCCUUCCGUUAGUUUUUAAUAAAAUUAUACAUGCAAGCUUCCACGCCCCAGUGAGAAUGCCCUUCAGAUCCCUACAGCCGAUCAAAAGGAGCGGGUAUCAAGCACACUCAACGAGUAGCUCACAACGCCUUGCUCAACCACACCCCCACGGGACACAGCAGUAAUAAAAAUUAAGCCAUGAACGAAAGUUCGACUAAGUUAUAUUAAUCAUAAGGGUUGGUAAAUUUCGUGCCAGCCACCGCGGUCAUACGAUUAACCCAAACUAACGGGCUCACGGCGUAAAGCGUGUAAAAGAUCUACCUACACUAAAGUUAAAAUUUAACCAAGCCGUAAAAAGCUGCCGUUAAUACAAAAUAUACUACGAAAGUGACUUUAAUAAUUCUGAUUACACGAUAGCUAAGACCCAAACUGGGAUUAGAUACCCCACUAUGCUUAGCCCUAAACAUAAAUAAUUCACUUAACAAAAUUAUCCGCCAGAGAACUACUAGCAAUAGCUUAAAACUCAAAGGACUUGGCGGUGCUUCACAUCCCCCUAGAGGAGCCUGUUCUAUAAUCGAUAAACCCCGAUAAACCUCACCACCUCUUGCUAAUCCAGUCUAUAUACCGCCAUCCUCAGCAAACCCUUAAAAGGAAAGAAAGUAAGCAUAAUCAUCGCACGUAAAAAAGUUAGGUCAAGGUGUAACCCAUGAGGUGGGAAGAAAUGGGCUACAUUUUCUAAACAAGAACACACCGUACGAAAGUUAUUAUGAAACUAAUAACUAAAGGUGGAUUUAGUAGUAAACUAAGAAUAGAGAGCUUAAUUGAACUGGGCCAUGAAGCACGCACACACCGCCCGUCACCCUCCUCAAAUAAUAACCUCAAAGCACAUACAUAAAUCAAUAUAAAACCAUAAGAGGAGAUAAGUCGUAACAAGGUAAGCAUACUGGAAAGUGUGCUUGGAUAAAU diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq new file mode 100644 index 0000000..10bd605 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.m.Z.mays.seq @@ -0,0 +1,2 @@ +>d.16.m.Z.mays +AAAAUCUGAGUUUGAUCCUGGCUCAGAAGGAACGCUAGCUAUAUGCUUAACACAUGCAAGUCGAACGUUGUUUUCGGGGAGCUGGGCAGAAGGAAAAGAGGCUCCUAGCUAAAGUUGUCUCGCCCUGCCUGCAGGGCGCGCGCAACGGCUUUGACCUAACGGCCUCCGUUUGCUGGAAUCGGAAUAGUUGAGAACAAAGUGGCGAACGGGUGCGUAACGCGUGGGAAUCUGCCGAACAGUUCGGGCCAAAUCCUGAAGAAAGCUCAAAAGCGCUGUUUGAUGAGCCUGCGUAGUAUUAGGUAGUUGGUCAGGUAAAGGCUGACCAAGCCAAUGAUGCUUAGCUGGUCUUUUCGGAUGAUCAGCCACACUGGGACUGAGACACGGCCCGGACUCCCACGGGGGGCAGCAGUGGGGAAUCUUGGACAAUGGGCGAAAGCCCGAUCCAGCAAUAUCGCGUGAGUGAAGAAGGGCAAUGCCGCUUGUAAAGCUCUUUCGUCGAGUGCGCGAUCAUGACAGGACUCGAGGAAGAAGCCCCGGCUAACUCCGUGCCAGCAGCCGCGGUAAGACGGGGGGGGCAAGUGUUCUUCGGAAUGACUGGGCGUAAAGGGCACGUAGGCGGUGAAUCGGGUUGAAAGUGAAAGUCGCCAAAAAGUGGCGGAAUGCUCUCGAAACCAAUUCACUUGAGUGAGACAGAGGAGAGUGGAAUUUCGUGUGUAGGGGUGAAAUCCGUAGAUCUACGAAGGAACGCCAAAAGCGAAGGCAGCUCUCUGGGUCCCUACCGACGCUGGGGUGCGAAAGCAUGGGGAGCGAACAGGAUUAGAUACCCUGGUAGUCCAUGCCGUAAACGAUGAGUGUUCGCCCUUGGUCUGUCUACGCUACGCUACGCGGAUCAGGGGCCCAGCUAACGCGUGAAACACUCCGCCUGGGGAGUACGGUCGCAAGACCGAAACUCAAAGGAAUUGACGGGGGCCUGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUACAACGCGCAAAACCUUACCAGCCCUUGACAUAUGAACAACAAAACCUGUCUUUAACGGGAUGGUACUUACUUUCAUACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUUGGUCAAGUCCUAUAACGAGCGAAACCCUCGUUUUGUGUUGCUGAGACAUGCGCCUAAGGAGAAAUAGCCGAGGAGCCGAGUGACGUGCCAGCGCUACUACUUGAUUGAGUGCCAGCACGUAGCUGUGCUUUCCGCAAGAAUUUCACCAUUGGGAGCCUCGAAGCACUUUCACGUGUGAACCGAAGUCGUCUUGCCGAACUCAAGACCCACGGAGACCUACCUAUAGUGACGUCAAAGUACCAGUGAGCAUGGAGGUUUGGUUAGGCUUGGUUACGACGACGUCGAGUUGGCGGCGGAGGAAGACUCGGCAUGAAGGCCAGCCGCCCGGUGGUGUGGUACGUAGUGGUAAUAGUACGCGCCCCGCUCCGAAACAAAGAAAAAGGUGCGUGCCGCACUCACGAGGGACUGCCAGUGAGAUACUGGAGGAAGGUGGGGAUGACGUCAAGUCCGCAUGGCCCUUAUGGGCUGGGCCACACACGUGCUACAAUGGCAAUGACAAUGGGAAGCAAGGCUGUAAGGCGGAGCGAAUCCGGAAAGAUUGCCUCAGUUCGGAUUGUUCUCUGCAACUCGGGAACAUGAAGUAGAAAUCGCUAGUAAUCGCGGAUCAGCAUGCCGCGGUGAAUAUGUACCCGGGCCCUGUACACACCGCCCGUCACACCCUGGGAAUUGGUUUCGCCCGAAGCAUCGGACCAAUGAUCACCCAUGACUUCUGUGUACCACUAGUGCCACAAAGGCCUUUGGUGGUCUUAUUGGCGCAUACCACGGUGGGGUCUUCGACUGGGGUGAAGUCGUAACAAGGUAGCCGUAGGGGAACCUGUGGCUGGAUUGAAUCCUUC diff --git a/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq b/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq new file mode 100644 index 0000000..48e9291 --- /dev/null +++ b/gtfold-mfe/tests/data/16S_sequences/d.16.y.C.paradoxa.seq @@ -0,0 +1,2 @@ +>d.16.y.C.paradoxa +UACCAUGGAGAGUUUGAUCCUGGCUCAGGAUGAACGCUGGCGGUAUGCUUAACACAUGCAAGUCGAACGAAGAUCGCAAGAUCUUAGUGGCGGACGGGUGAGUAACGCGUGAGAAUCUACCCUUAGGAGGGGGACAACAGUUGGAAACGACUGCUAAUACCCCAUAUGCCAUUCGUGGUGAAAAGAGUAAUCUGCCUGAGGAAGAGCUCGCGUCUGAUUAGCUAGUUGGUGGGGUAAAGGCCUACCAAGGCGACGAUCAGUAGCUGGUCUGAGAGGAUGAUCAGCCACACUGGGACUGAGAUACGGCCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUUUUCCGCAAUGGGCGAAAGCCUGACGGAGCAAUACCGCGUGAGGGAAGACGGCCUGUGGGUUGUAAACCUCUUUUCUUAGGGAAGAAUCAAUGACGGUACCUAAGGAAUAAGCAUCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGAUGCAAGCGUUAUCCGGAAUCAUUGGGCGUAAAGAGUUCGUAGGUGGCUAAGCAAGUCUGUUGUUAAAGGCUGGGGCUUAACCCCAAAAAGGCAAUGGAAACUGUUUGGCUUGAGUACGGUAGGGGCAGAGGGAAUUCCUGGUGUAGCGGUGAAAUGCGUAGAUAUCAGGAAGAACACCGAUGGCGAAAGCACUCUGCUGGGCCGUUACUGACACUGAGGAACGAAAGCUAGGGUAGCAAAUGGGAUUAGAUACCCCAGUAGUCCUAGCCGUAAACUAUGGAUACUAGGUGUUGUGCGUAUCGACCCGUACAGUACCGUAGCUAACGCGUUAAGUAUCCCGCCUGGGGAGUACGCUCGCAAGAGUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGUAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCAGGGUUUGACAUGUCGCGAAUUUUCUUGAAAGAGAAAAGUGCCUUCGGGAACGCGAACACAGGUGGUGCAUGGCUGUCGUCAGCUCGUGUCGUGAGAUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCUCGUUUUUAGUUGCCAUCAUUCAGUUGGGCACUCUAAAGAGACUGCCGGUGACAAGCCGGAGGAAGGUGGGGAUGACGUCAAGUCAGCAUGCCCCUUAUACCCUGGGCUACACACGUACUACAAUGGUCGGGACAAUAGGUUGCCAACUUGCGAAAGUGAGCUAAUCCGUUAAACCCGGCCUCAGUUCAGAUUGCAGGCUGCAACUCGCCUGCAUGAAGGUGGAAUCGCUAGUAAUCGCCGGUCAGCUAUACGGCGGUGAAUUCGUUCCCGGGCCUUGUACACACCGCCCGUCACACCACGGGAGUCGGCCAUGCCCGAAGUCGUUACCCUAACCAUUUCGGAGGGGGAUGCCUAAGGCAGGGCUGGUGACUGGGGUGAAGUCGUAACAAGGUAGCCGUACUGGAAGGUGCGGCUGGAUCACCUCCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq new file mode 100644 index 0000000..84b1c04 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.D.mobilis.seq @@ -0,0 +1,2 @@ +>d.5.a.D.mobilis +ACGGUGCCCGACCCGGCCAUAGUGGCCGGGCAACACCCGGUCUCGUUUCGAACCCGGAAGUUAAGCCGGCCACGUCAGAACGGCCGUGAGGUCCGAGAGGCCUCGCAGCCGUUCUGAGCUGGGAUCGGGCACC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq new file mode 100644 index 0000000..d202539 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.marismortui.seq @@ -0,0 +1,2 @@ +>d.5.a.H.marismortui +UUAGGCGGCCACAGCGGUGGGGUUGCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCACCAGCGUUCCGGGGAGUACUGGAGUGCGCGAGCCUCUGGGAAACCCGGUUCGCCGCCACC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq new file mode 100644 index 0000000..1bfbb69 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.mediterranei.1.seq @@ -0,0 +1,2 @@ +>d.5.a.H.mediterranei.1 +AUUAGGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCGCCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq new file mode 100644 index 0000000..637ed19 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.1.seq @@ -0,0 +1,2 @@ +>d.5.a.H.morrhuae.1 +UUAAGGCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUGGUUCGCCGCCUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq new file mode 100644 index 0000000..1dd9dcf --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.morrhuae.2.seq @@ -0,0 +1,2 @@ +>d.5.a.H.morrhuae.2 +UUAAGGCGGCCACAGCGGCGGGGCGACUCCCGUACCCAUCCCGAACACGGCAGAUAAGCCCGCCAGCGUUCCAGCGAGUACUGGAGUGUGCGAACCUCUGGGAAAACUGGUUCGCCGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq new file mode 100644 index 0000000..dba1e06 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.saccharovorum.seq @@ -0,0 +1,2 @@ +>d.5.a.H.saccharovorum +GGCAGCGGCCAUAGCGGUGGGGCGACACCCGUACCCAUUCCGAACACGGAAGUUAAGCCCACCAGCGUACCGGGAAGUACUGGAGUGAGCGAUCCUCUGGGAAGCGGGGUUCGCCGCCUGCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq new file mode 100644 index 0000000..13aca4b --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.1.seq @@ -0,0 +1,2 @@ +>d.5.a.H.salinarum.1 +UUAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq new file mode 100644 index 0000000..cd1707d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.salinarum.2.seq @@ -0,0 +1,2 @@ +>d.5.a.H.salinarum.2 +UUAAGGCGGCCAUAGCGGUGGGGUUACUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCCGCCUGCGUUCCGGUCAGUACUGGAGUGCGCGAGCCUCUGGGAAAUCCGGUUCGCCGCCUACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq new file mode 100644 index 0000000..149b7b4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.H.volcanii.seq @@ -0,0 +1,2 @@ +>d.5.a.H.volcanii +UUAAGGCGGCCAGAGCGGUGAGGUUCCACCCGUACCCAUCCCGAACACGGAAGUUAAGCUCACCUGCGUUCUGGUCAGUACUGGAGUGAGCGAUCCUCUGGGAAAUCCAGUUCGCCGCCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq new file mode 100644 index 0000000..aa89660 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.barkeri.seq @@ -0,0 +1,2 @@ +>d.5.a.M.barkeri +GGAGUUUGGCGCCAUAGCGGCAGUGUAACUCCUGUACCCAUCCCGAACACAGUAGAUAAGCCUGCCCGCGUUCCUUACUGUACUGAAGUGUGCGAGCCUUCGGGAACUCUGGAUCGCUGCCAUACUCACC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq new file mode 100644 index 0000000..014e2e9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.fervidus.seq @@ -0,0 +1,2 @@ +>d.5.a.M.fervidus +GGGUACGGCGACCAUAGCGGGGGGGCCACACCUGAACCCGUUCCGAUCUCAGAAGUUAAGCCCCCCUGCGUUGGAGGUGGUACUGCAACGUUAGUUGCGGGAAGCCUCCAACGUCGCCGGCCCA diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq new file mode 100644 index 0000000..0d9789e --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.formicicum.seq @@ -0,0 +1,2 @@ +>d.5.a.M.formicicum +AGGUUGGCGGCCAUAGCGGAGGGGCCAUACCUGGUCUCGUUUCGAUCCCAGAAGUGAAGUCCUCCUGCGUUUUGUUGUUGUACUGUGGACGAGAGUCUAUGGGAAGCUCAUAACGCUGCCGGCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq new file mode 100644 index 0000000..173a5b8 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnA.seq @@ -0,0 +1,2 @@ +>d.5.a.M.jannaschii.rrnA +UGGUACGGCGGUCAUAGCGGGGGGGCCACACCCGAACCCAUCCCGAACUCGGAAGUUAAGCCCCCCAGCGAUGCCCCGAGUACUGCCAUCUGGCGGGAAAGGGGCGACGCCGCCGGCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq new file mode 100644 index 0000000..8df9051 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.jannaschii.rrnB.seq @@ -0,0 +1,2 @@ +>d.5.a.M.jannaschii.rrnB +UGGUACGGCGGUCAUAGCGGGGGGGCCACACCCGAACCCAUCCCGAACUCGGAAGUUAAGCCCCCCAGCGAUGCCCCGAGUACUGCCAUCUGGCGGGAAAGGGGCGACACCGCCGGCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq new file mode 100644 index 0000000..ac65026 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermautotrophicus.1.seq @@ -0,0 +1,2 @@ +>d.5.a.M.thermautotrophicus.1 +GGGGCAUGGCGGUCAUGGCGCAGGGGUUAUACCUGAUCUCGUUUCGAUCUCAGUAGUUAAGUCCUGCUGCGUUGUGGGUGUGUACUGCGGUUUUUUGCUGUGGGAAGCCCACUUCACUGCCAGCCACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq new file mode 100644 index 0000000..2c27595 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.thermolithotrophicus.2.seq @@ -0,0 +1,2 @@ +>d.5.a.M.thermolithotrophicus.2 +UGAUAUAACGGUCAUAGCGGAGGAGCCACAUCCGAUCCCGUCCCGAUCUCGGAAAUUAAGCCCUCCAGCGAUACCCUAAGUACUGCCAUUUGGUGGGAACAGGGUGACGCUGUUGAUCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq new file mode 100644 index 0000000..bc9a31f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.tindarius.1.seq @@ -0,0 +1,2 @@ +>d.5.a.M.tindarius.1 +GGAGUUUGGCGGCCAUAGCGGCGGGGCAAUUCCUGUACCCAUCCCGAACACAGAAGAUAAGCCCGCCUGCGUUCUAUACUGUACUAAAGUAUGAGAGUCUUUGGGAAAUAUGGAACGCUGCCAUCUCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq new file mode 100644 index 0000000..2289727 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.M.vacuolata.seq @@ -0,0 +1,2 @@ +>d.5.a.M.vacuolata +GAUCUGGCAGCCAUAGCGGCAGGUGUAAUCCUGUACCCAUCCCGAACACAGUAGAUAAGCCUGCCCGCGUUCCUUGCCUGUACUGAAGUGUGCGAGCUUCGGGAACUCUGGAUCGUGCCAUAUCAGU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq new file mode 100644 index 0000000..1e9fb96 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.N.magadii.seq @@ -0,0 +1,2 @@ +>d.5.a.N.magadii +UUAAGGCGGCCAUCGCGGCGGGGUUCCUCCCGUACCCAUCCCGAACACGGAAGAUAAGCCUGCCUGCGUAUUGGUGAGUACUGGAGUGGGAGACCCUCUGGGAGAGCCGAUUCGCCGCCCCUACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq new file mode 100644 index 0000000..35940f9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.aerophilum.seq @@ -0,0 +1,2 @@ +>d.5.a.P.aerophilum +GCCCCUAACCCGGCCAUAGGCGCCGGUGAUACGCCCGGUCUCAUCAGAACCCGGAAGCUAAGGCCGGCGCCGCGCUCGGGAGUACUGGGCUCCGCGAGGGCCCGGGAAACCGGCGUGCUGGGAGGGGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq new file mode 100644 index 0000000..fe1e44d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.occultum.seq @@ -0,0 +1,2 @@ +>d.5.a.P.occultum +UGGCCCGACCCGGCCAUAGCGGCCGGGCAACACCCGGACUCAUGUCGAACCCGGAAGUUAAGCCGGCCGCGUUGGGGGAUGCUGUGGGGUCCGCGAGGCCCCGCAGCGCCCCCAAGCCGGGAUCGGGCCG diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq new file mode 100644 index 0000000..0db6b35 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.P.woesei.seq @@ -0,0 +1,2 @@ +>d.5.a.P.woesei +GGUACGGCGGUCAUAGCGGGGGGGCCACACCCGGUCUCAUUUCGAACCCGGAAGUUAAGCCCCCCAGCGAUCCCGGCUGUACUGCCCUCCGAGAGGGGGCGGGAACCGGGGACGCCGCCGGCCA diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq new file mode 100644 index 0000000..5e79dbe --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.S.solfataricus.seq @@ -0,0 +1,2 @@ +>d.5.a.S.solfataricus +GCCCACCCGGUCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUAGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAUGGGUUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq new file mode 100644 index 0000000..993246c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.Sulfolobus.sp.B12.seq @@ -0,0 +1,2 @@ +>d.5.a.Sulfolobus.sp.B12 +GCCCACCCGGCCACAGUGAGCGGGCAACACCCGGACUCAUUUCGAACCCGGAAGUUAAGCCGCUCACGUUGGUGGGGCCGUGGAUACCGUGAGGAUCCGCAGCCCCACUAAGCUGGGAUGGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq new file mode 100644 index 0000000..a7dad6b --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.acidophilum.seq @@ -0,0 +1,2 @@ +>d.5.a.T.acidophilum +GGCAACGGUCAUAGCAGCAGGGAAACACCAGAUCCCAUUCCGAACUCGACGGUUAAGCCUGCUGCGUAUUGCGUUGUACUGUAUGCCGCGAGGGUACGGGAAGCGCAAUAUGCUGUUACCACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq new file mode 100644 index 0000000..91d9b16 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.a.T.celer.1.seq @@ -0,0 +1,2 @@ +>d.5.a.T.celer.1 +GGUACGGCGGUCAUAGCGGCGGGGUCACACCCGGUCUCGUUUCGACCCCGGAAGUUAAGCCCGCCAGCGAUCCCGGUUGUACUGCCCUCCGGGAGGGGGCGGGAAGCCGGGGACGCCGCCGGCCACU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq new file mode 100644 index 0000000..758f2f3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.A.tumefaciens.seq @@ -0,0 +1,2 @@ +>d.5.b.A.tumefaciens +CGACCUGGUGGUCAUCGCGGGGCGGCUGCACCCGUUCCCUUUCCGAACACGGCCGUGAAACGCCCCAGCGCCAAUGGUACUUCGUCUCAAGACGCGGGAGAGUAGGUCGCUGCCAGGUCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq new file mode 100644 index 0000000..42aafa3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.D.radiodurans.rrnB.seq @@ -0,0 +1,2 @@ +>d.5.b.D.radiodurans.rrnB +ACACCCCCGUGCCCAUAGCACUGUGGAACCACCCCACCCCAUGCCGAACUGGGUCGUGAAACACAGCAGCGCCAAUGAUACUCGGACCGCAGGGUCCCGGAAAAGUCGGUCAGCGCGGGGGUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq new file mode 100644 index 0000000..c43add3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.E.coli.seq @@ -0,0 +1,2 @@ +>d.5.b.E.coli +UGCCUGGCGGCCGUAGCGCGGUGGUCCCACCUGACCCCAUGCCGAACUCAGAAGUGAAACGCCGUAGCGCCGAUGGUAGUGUGGGGUCUCCCCAUGCGAGAGUAGGGAACUGCCAGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq new file mode 100644 index 0000000..215d002 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.2.seq @@ -0,0 +1,2 @@ +>d.5.b.G.stearothermophilus.2 +CCUAGUGGUGAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCCUCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGUCGCUGCUAGGC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq new file mode 100644 index 0000000..c061b92 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.3.seq @@ -0,0 +1,2 @@ +>d.5.b.G.stearothermophilus.3 +CCUAGUGACAAUAGCGAGAGAGGAAACACCCGUCUCCAUCCCGAACACGAAGGUUAAGCUCUCCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGUUGUCGCUAGGC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq new file mode 100644 index 0000000..c3fb93d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.G.stearothermophilus.4.seq @@ -0,0 +1,2 @@ +>d.5.b.G.stearothermophilus.4 +CCUAGUGGUGAUAGCGGAGGGGAAACACCCGUUCCCAUCCCGAACACGGAAGUUAAGCCCUCCAGCGCCGAUGGUAGUUGGGGCCAGCGCCCCUGCAAGAGUAGGCCGCUGCUAGGC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq new file mode 100644 index 0000000..f3cf935 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.b.M.genitalium.seq @@ -0,0 +1,2 @@ +>d.5.b.M.genitalium +UUUUGUUUGGUGCUAAUAUCGCUGUGGAAACACCUGGAACCAUCCCGAACCCAGCAGUUAAGCACAGUGGAGCUAAAUGUAGGUAGUAAUACUGAGAAUAGGUAAGCACCAAGCAAAA diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq new file mode 100644 index 0000000..2eb8001 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aquaticus.seq @@ -0,0 +1,2 @@ +>d.5.e.A.aquaticus +GUCAACGGCCAUACCACGUUGAAAGCACCGCUUCUCGUCCGAUCAGCAAAGUUAAGCAACGUUGGGUCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAACACCAGAUGCUGUUGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq new file mode 100644 index 0000000..4691f30 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.aurita.2.seq @@ -0,0 +1,2 @@ +>d.5.e.A.aurita.2 +GCCUACGACUAUACCACCAUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUUAAGUAUGGUAGGGCCGGGUCAGUACCUGGAUGGGUGACCGCCUGGGAACACCCGGUGUUGUAGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq new file mode 100644 index 0000000..21ffcae --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.domesticus.seq @@ -0,0 +1,2 @@ +>d.5.e.A.domesticus +GCCAACGUCCAUACCACGUUGAAAGCACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAGCGUCGGGCGCGGUUAGUACUUGGAUGGGUGACCGCCUGGGAACCCCGCGUGACGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq new file mode 100644 index 0000000..e343cc3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.equina.seq @@ -0,0 +1,2 @@ +>d.5.e.A.equina +GUCUACGGCCAUACCACCGGGAAAAUACCGGUUCUCGUCCGAUCACCGAAGUCAAGCCCGGUAGGGCCAGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCUGGUGCUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq new file mode 100644 index 0000000..0b3da01 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.immersus.1.seq @@ -0,0 +1,2 @@ +>d.5.e.A.immersus.1 +ACAUACGGCCAUAGAUUGAAGAAUAUACGGGAUCCCGUCCGCUCUCCCAUAGUCAAGCUUCUAAUCGCCAAGUUAGUACUGCGGUGGGUGACCACGCGGGAAUCCUUGGUGCUGUAUGU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq new file mode 100644 index 0000000..336539c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.magnoliae.seq @@ -0,0 +1,2 @@ +>d.5.e.A.magnoliae +GGCAACGACCAUACCACGUUGAAUACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCGUAGUUAGUACUUGGAUGGGUGACCGCUUGGGAACACUACGUGCCGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq new file mode 100644 index 0000000..8b924c3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.pernyi.seq @@ -0,0 +1,2 @@ +>d.5.e.A.pernyi +GACAACGUCCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGGGCGCGGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACCGCGUGACGUUGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq new file mode 100644 index 0000000..bd70eab --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.salina.seq @@ -0,0 +1,2 @@ +>d.5.e.A.salina +ACCAACGGCCAUACCACGUUGAAAGUACCCAGUCUCGUCAGAUCCUGGAAGUCACACAACGUCGGGCCCGGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACCGGGUGCUGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq new file mode 100644 index 0000000..311e3c2 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.A.tabira.seq @@ -0,0 +1,2 @@ +>d.5.e.A.tabira +GCUUACAGCCAUACUGUCCUGAGCACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGACAAGGCCUGGUUAGUACUUGGAUGGGAGACUGCCUGGGAAUACCAGGUGCUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq new file mode 100644 index 0000000..b3d1240 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.napus.seq @@ -0,0 +1,2 @@ +>d.5.e.B.napus +GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq new file mode 100644 index 0000000..c94dd69 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.neritina.seq @@ -0,0 +1,2 @@ +>d.5.e.B.neritina +GUUUACGGCCAUAUCACGUUGAAAACGCCAGUUCUCGUCCGAUCACUGAAGCUAAGCAACGUCGAGCCUGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCAGGUGCUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq new file mode 100644 index 0000000..0f615ff --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.taurus.seq @@ -0,0 +1,2 @@ +>d.5.e.B.taurus +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq new file mode 100644 index 0000000..7d2da47 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vorax.seq @@ -0,0 +1,2 @@ +>d.5.e.B.vorax +GUUAUCGGCCAUACUAAGCCAAAAGCACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGGCUUAAGGCAUGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGCCCAUGUGCUGAUAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq new file mode 100644 index 0000000..a05bd88 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.B.vulgaris.seq @@ -0,0 +1,2 @@ +>d.5.e.B.vulgaris +GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq new file mode 100644 index 0000000..32ee26d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.carpio.seq @@ -0,0 +1,2 @@ +>d.5.e.C.carpio +GCUUACGGCCAUACCACCCUGAGCACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq new file mode 100644 index 0000000..91c3d86 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.1.seq @@ -0,0 +1,2 @@ +>d.5.e.C.elegans.1 +GCUUACGACCAUAUCACGUUGAAUGCACGCCAUCCCGUCCGAUCUGGCAAGUUAAGCAACGUUGAGUCCAGUUAGUACUUGGAUCGGAGACGGCCUGGGAAUCCUGGAUGUUGUAAGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq new file mode 100644 index 0000000..4a4584e --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.elegans.2.seq @@ -0,0 +1,2 @@ +>d.5.e.C.elegans.2 +GCUUACGACCAUAUCACGUUGAAUGCACGCCAUCCCGUCCGAUCUGGCAAGUUAAGCAACGUUGAGUCCAGUUAGUACUUGGAUCGGAGACGGCCUGGGAAUCCUGGAUGUUGUAAGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq new file mode 100644 index 0000000..4eef3e3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.quinquecirrha.seq @@ -0,0 +1,2 @@ +>d.5.e.C.quinquecirrha +GCCUACGACCAUACCACCAUGAGUAUACCGGUUCUCGUCCGAUCACCGGAGUCAAGCAUGGUCGGGCCGGGUCAGUACCUGGAUGGGUGACCGCCUGGGAACACCUGGUGUUGUAGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq new file mode 100644 index 0000000..0a9db8c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.revoluta.seq @@ -0,0 +1,2 @@ +>d.5.e.C.revoluta +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGUUGGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUAAUAUUGCACCCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq new file mode 100644 index 0000000..b9bba74 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.C.vicina.seq @@ -0,0 +1,2 @@ +>d.5.e.C.vicina +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq new file mode 100644 index 0000000..fe798c7 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.mauritiana.seq @@ -0,0 +1,2 @@ +>d.5.e.D.mauritiana +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq new file mode 100644 index 0000000..2a8d663 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.1.seq @@ -0,0 +1,2 @@ +>d.5.e.D.melanogaster.1 +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGCGGGCGGUUAGUACUUAGAUGGGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq new file mode 100644 index 0000000..05ba8f8 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.D.melanogaster.2.seq @@ -0,0 +1,2 @@ +>d.5.e.D.melanogaster.2 +GCCAACGACCAUACCACGCUGAAUACAUCGGUUCUCGUCCGAUCACCGAAAUUAAGCAGCGUCGGGCGCGGUUAGUACUUAGAUGAGGGACCGCUUGGGAACACCGCGUGUUGUUGGCCUCGUCCACAACUUUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq new file mode 100644 index 0000000..e715502 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.eurystomus.seq @@ -0,0 +1,2 @@ +>d.5.e.E.eurystomus +GCUAUCGGCCAUACUAAGCCAAAUGCACCGGAUCCCUUCCGAACUCCGAAGUUAAGCGGUUUAAGGCCUGUUAAGUACUGAGGUGGGGGACCACUCGGGAACUUCAGGUGCUGAUAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq new file mode 100644 index 0000000..c73a6b7 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.1.seq @@ -0,0 +1,2 @@ +>d.5.e.E.gracilis.1 +GAGUACGGCCAUACUACCGGGAAUACACCUGAACCCGUUCGAUUUCAGAAGUUAAGCCGGGUUAGGCCCAGUUAGUACUGAGUGGGCGACCACUUGGGAACACUGGGUGCUGUACGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq new file mode 100644 index 0000000..895e4e4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.gracilis.2.seq @@ -0,0 +1,2 @@ +>d.5.e.E.gracilis.2 +GGCGUACGGCCAUACUACCGGGAAUACACCUGAACCCGUUCGAUUUCAGAAGUUAAGCCUGGUCAGGCCCAGUUAGUACUGAGGUGGGCGACCACUUGGGAACACUGGGUGCUGUACGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq new file mode 100644 index 0000000..33c38fc --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.kokanica.seq @@ -0,0 +1,2 @@ +>d.5.e.E.kokanica +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq new file mode 100644 index 0000000..2b22082 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.E.woodruffi.seq @@ -0,0 +1,2 @@ +>d.5.e.E.woodruffi +GCUAUCGGCCAUACUAAGCCAAAUGCACCGGAUCCCAUCCGAACUCCGAAGUUAAGCGGUUUAAGGCCUGUUAAGUACUGAGGUGGGGGACCACUCGGGAACUUCAGGUGCUGAUAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq new file mode 100644 index 0000000..946b73c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.hygrometrica.seq @@ -0,0 +1,2 @@ +>d.5.e.F.hygrometrica +UGAUGCGGUCAUACCAAGGCUACUACACCAGAUCCCAUCAGAACUCUGAAGUUAAGCGCCUUUGGGCCGGAAUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCCGGUGCUGCAUCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq new file mode 100644 index 0000000..30eaebf --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.F.neoformans.1.seq @@ -0,0 +1,2 @@ +>d.5.e.F.neoformans.1 +AUCCACGGCCAUAGCCUUCAUAGAGCACCCUGCCCCGUCCGAUCCAGGAAGUUAAGCUGAACAGCGCUCGGUUAGUACCACGGUGGGGGACCACGUGGGAAUCCCGGGUGCCGUGGUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq new file mode 100644 index 0000000..7b952b0 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.arboreum.seq @@ -0,0 +1,2 @@ +>d.5.e.G.arboreum +GGGUGCGAUCAUACCAGCACUAAACCACCGGAUUCCAUCAGUGCUCCCCAGUUAAGCGUGCUUGGCCGAGAGUAGAACUAGGGUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq new file mode 100644 index 0000000..cb7eb79 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.biloba.seq @@ -0,0 +1,2 @@ +>d.5.e.G.biloba +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCACGCUUGGGCUGGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCCAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq new file mode 100644 index 0000000..178c783 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.gnemon.seq @@ -0,0 +1,2 @@ +>d.5.e.G.gnemon +GGGUGCGAUAAUACCACCGCUAACGUAUCGGAUCCGAUCAGAACUCCGUAAUUAAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCUCGGGAAGUCCUAGUGUUGCACCCAC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq new file mode 100644 index 0000000..1d478a3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.G.riobambae.seq @@ -0,0 +1,2 @@ +>d.5.e.G.riobambae +GCCUACGGCCACACCACCCUGAACACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq new file mode 100644 index 0000000..f67da34 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.japonica.seq @@ -0,0 +1,2 @@ +>d.5.e.H.japonica +GUCUACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGGGCCUGCCCAGUACUUGGAUGGGUGACCGCCUGGGAACAGCAGGUGUUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq new file mode 100644 index 0000000..49bf2a1 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.oculata.seq @@ -0,0 +1,2 @@ +>d.5.e.H.oculata +GCCUGCGGCCAUACCACGUUGAAUGCACCGGUUCCCAUCUGAACACCGAAGUUAAGCAACGUCGGGCCAGCUUAGUACCUGGAUGGGUGACCGCCUGGGAAUCGCUGGUGCUGCAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq new file mode 100644 index 0000000..55c19b9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sanguinea.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sanguinea +GUCUACGACCAUACCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGGGCCUGCCCAGUACUUGGAUGGGUGACCGCCUGGGAACAGCAGGUGUUGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq new file mode 100644 index 0000000..517c965 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.1.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.1 +AUCUAUGGCUGUACCGCUCUGAACGUGCACUAUCUCUUCUGAUCUCAAAAGCUAAGCAGGGUCAGGCCUGGUUAGUACUGGAAUGGGAGACCACAUGGGAAAACUGGGUGCUGUAGGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq new file mode 100644 index 0000000..1b449fa --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.2.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.2 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq new file mode 100644 index 0000000..d82f578 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.3.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.3 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq new file mode 100644 index 0000000..fdcdc80 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.4.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.4 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq new file mode 100644 index 0000000..627f910 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.5.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.5 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq new file mode 100644 index 0000000..01812e1 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.H.sapiens.6.seq @@ -0,0 +1,2 @@ +>d.5.e.H.sapiens.6 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq new file mode 100644 index 0000000..a8577d9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Hemicentrotus.sp.seq @@ -0,0 +1,2 @@ +>d.5.e.Hemicentrotus.sp +GUUUACGACCAUACCAUGCUGAAUAUACCGGUUCUCGUCCGAUCACCGAAGUCAAGCAGCAUAGGGCCCGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGUUGUAGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq new file mode 100644 index 0000000..fb02dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.iguana.seq @@ -0,0 +1,2 @@ +>d.5.e.I.iguana +GCCUACGGCCAUACCACCCUGAACACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq new file mode 100644 index 0000000..39aa1e2 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.I.illecebrosus.seq @@ -0,0 +1,2 @@ +>d.5.e.I.illecebrosus +GCUUACGGCCAUAUCACGCUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUAGAGCCUAGUCAGUACUUGGAUGGGUGACCGCCUGGGAAUACUAGGUGCUGUAAGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq new file mode 100644 index 0000000..9a40744 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.decidua.seq @@ -0,0 +1,2 @@ +>d.5.e.L.decidua +GGGUGCGAUCAUACCAGCGUUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCACGCUUGGGCUAGAGUAGUGCUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq new file mode 100644 index 0000000..2d9f606 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.edodes.seq @@ -0,0 +1,2 @@ +>d.5.e.L.edodes +AUCCACGGCCAUAGGACUCUGAAAGAACCGCAUCCCGUCUGAUCUGCGCAGUUAACCAGAGUGCCGCCUAGUUAGUACCACGGUGGGGGACCACGCGGGAAUCCUAGGUGCUGUAGUUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq new file mode 100644 index 0000000..73c1db0 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.geniculatus.seq @@ -0,0 +1,2 @@ +>d.5.e.L.geniculatus +GUCUACGACCAUAUCACGUUGAAAACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAACGUCGAGCGUGGUUAGUACGUGGAUGGGUGACCGCCUCGGAAUACCACGUGUUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq new file mode 100644 index 0000000..83e9877 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.japonicum.seq @@ -0,0 +1,2 @@ +>d.5.e.L.japonicum +GCCUACGACCAUAUCACCCUGAAUACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGAGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGUUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq new file mode 100644 index 0000000..9d33a3c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.luteus.seq @@ -0,0 +1,2 @@ +>d.5.e.L.luteus +AGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCUCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq new file mode 100644 index 0000000..2e8a669 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.L.usitatissimum.seq @@ -0,0 +1,2 @@ +>d.5.e.L.usitatissimum +GGGUGCGAUCAUACCAGCACUAAUGCACCGGAUCCCAUCAGAACUCCGAAGUUAAACGUGCUUGGGCGAGAGUAGUACUAAGAUGGGUGACCUCUUGGGAAGUCCUCGUGUUGCACCCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq new file mode 100644 index 0000000..dfa7faa --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.auratus.seq @@ -0,0 +1,2 @@ +>d.5.e.M.auratus +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq new file mode 100644 index 0000000..046a55c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.fossilis.seq @@ -0,0 +1,2 @@ +>d.5.e.M.fossilis +GCUUACGGCCAUACCACCCUGAGCACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACUGCCUGGGAAUACCAGGUGUUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq new file mode 100644 index 0000000..1d4c204 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.glyptostroboides.seq @@ -0,0 +1,2 @@ +>d.5.e.M.glyptostroboides +GGGUGCGAUCAUACCAGCGUUAGUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGCGCUUGGGCCGGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCCGGUAUUGCACCCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq new file mode 100644 index 0000000..fa29c33 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.musculus.seq @@ -0,0 +1,2 @@ +>d.5.e.M.musculus +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq new file mode 100644 index 0000000..3101592 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.M.salmoides.seq @@ -0,0 +1,2 @@ +>d.5.e.M.salmoides +GCUUACGGCCACACCACCCUGAACACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGUCGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq new file mode 100644 index 0000000..df2ff9f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.dofleini.seq @@ -0,0 +1,2 @@ +>d.5.e.N.dofleini +GUCUACGACCAUACCACAAUGAACACACCGGUUCUCGUCCGAUCACCGAAGUUAAGCAUUGUCGGGCCAGGAUAGUACCUGGAUGGGGGACCGCCUGGGAACGCCUGGUGUCGUAGACUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq new file mode 100644 index 0000000..a966f10 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.N.viridescens.seq @@ -0,0 +1,2 @@ +>d.5.e.N.viridescens +GCUUACGGCCAUACCACCCUGAAAGCACCUGAUCUCGUCUGAUCUCAGAAGUUAAGCAGGGUCGGGCCUGGUUAGUACCUGGAUGGGAGACCGCCUUGGAAUACCAGGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq new file mode 100644 index 0000000..0f05eee --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.mykiss.seq @@ -0,0 +1,2 @@ +>d.5.e.O.mykiss +GCUUACGGCCAUACCAGCCUGAAUACGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAAGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq new file mode 100644 index 0000000..614084f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.1.seq @@ -0,0 +1,2 @@ +>d.5.e.O.sativa.1 +GGAUGCGAUCAUACCAGCACUAAAGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUUGUGUUGCAUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq new file mode 100644 index 0000000..bb31e0b --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.O.sativa.2.seq @@ -0,0 +1,2 @@ +>d.5.e.O.sativa.2 +GGAUGCGAUCAUACGAGGACGAAAGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUUGUGUUGCAUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq new file mode 100644 index 0000000..9c4e025 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.brevicirris.seq @@ -0,0 +1,2 @@ +>d.5.e.P.brevicirris +GCCUACGGCCAUACUACGUUGAAAACACCGGUUCUCGUCUGAUCACCGAAGUUAAGCAACGUCGGGCCUGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCAGGUGCUGUAGGUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq new file mode 100644 index 0000000..035e1ec --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.coxalis.seq @@ -0,0 +1,2 @@ +>d.5.e.P.coxalis +GUCAACGGCCAUACCACGUUGAAAGCACCACUUCUCGUCCGAUCAGCGAAGUUAAGCAACGUUGGGUCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAACACCAGAUGCUGUUGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq new file mode 100644 index 0000000..bb21939 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.gouldii.seq @@ -0,0 +1,2 @@ +>d.5.e.P.gouldii +GCCUACGACCAUACCACGUUGAAAACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCCAGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCUGGUGUUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq new file mode 100644 index 0000000..cee3f47 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.1.seq @@ -0,0 +1,2 @@ +>d.5.e.P.hybrida.1 +GGAUGCGAUCAUACCAGCACUAACGCACCGGAUCCCAUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUGGAAUGGGUGACCCUCCGGGAAGUCCUCGUGUUGCAUCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq new file mode 100644 index 0000000..4b4969f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.hybrida.2.seq @@ -0,0 +1,2 @@ +>d.5.e.P.hybrida.2 +AGAUGCGAUCAUACCAGCACUAACGCACCGGAUCCCAUCAGAACUCCGAAGCUAAGCGUGCUUGGGCGAGAGUAGUACUGGAAUGGGUGACCCUCCGGGAAGUCCUCGUGUUGCAUCCCG diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq new file mode 100644 index 0000000..0fe2e5f --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.radiata.seq @@ -0,0 +1,2 @@ +>d.5.e.P.radiata +GGGUGCGAUCAUACCAGCGUUAAUGCACCGAAUCCCAUCAGAACUCCGCAGUUUAGCGCGCUUGGGCUAGAGUAGUACUGGGAUGGGUGACCUCCCGGGAAGUCCUAGUGUUGCACCCUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq new file mode 100644 index 0000000..48aafa5 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.reticulata.seq @@ -0,0 +1,2 @@ +>d.5.e.P.reticulata +GAUAGCGUCCAUACCACACUGAAAACACCGGUUCUCGUCCGAUCACCGCAGUUAAGCAGUGUCGGGCCCAGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACUGGGUGUCGCUACCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq new file mode 100644 index 0000000..ac85b0c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.tetraurelia.seq @@ -0,0 +1,2 @@ +>d.5.e.P.tetraurelia +GUUGGUGGCCAUACUAAGCCUAAAGCACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGGCUUAAGGCGAGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGUCCUCGUGUUGACAACCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq new file mode 100644 index 0000000..686043c --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.P.waltl.seq @@ -0,0 +1,2 @@ +>d.5.e.P.waltl +GCCUACGGCCAUACCACCCUGAAUGCGCCCGAUCUCGUCCGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCUGUAGGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq new file mode 100644 index 0000000..7356089 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Phytomonas.sp.seq @@ -0,0 +1,2 @@ +>d.5.e.Phytomonas.sp +GGGUACGACCAUACUUGGCUGAAAGCACCACAUCCCGUCCGAUUUGUGAAGUUAAGCAGCCACAGGCUUAGUUAGUACUGAGGUCAGUGAUGACUCGGGAACCCUGAGUGCCGUACCCUCCACAACACUC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq new file mode 100644 index 0000000..4611843 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.Q.petraea.seq @@ -0,0 +1,2 @@ +>d.5.e.Q.petraea +GGGUGCGAUCAUACCAACACUAAUGCACCGGAUCCCAUCAGAACUCCGCAGUUAAGCGUGUUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUGGGAAGUCCUCGUGUUGCACCCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq new file mode 100644 index 0000000..b317aac --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.1.seq @@ -0,0 +1,2 @@ +>d.5.e.R.norvegicus.1 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq new file mode 100644 index 0000000..9bfefd4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.2.seq @@ -0,0 +1,2 @@ +>d.5.e.R.norvegicus.2 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq new file mode 100644 index 0000000..97d8ffd --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.R.norvegicus.3.seq @@ -0,0 +1,2 @@ +>d.5.e.R.norvegicus.3 +GUCUACGGCCAUACCACCCUGAACGCGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGGGUCGGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCGGGUGCUGUAGGCUUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq new file mode 100644 index 0000000..91ab62d --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.aggregatum.seq @@ -0,0 +1,2 @@ +>d.5.e.S.aggregatum +ACAGCCGUUCAUACCACACGGAGAAUACCGGAUCUCGUUCGAACUCCGCAGUCAAGCCGUGUCGGGCGUGCUCAGUACUACCAUAGGGGACUGGGUGGGAAGCGUGCGUGACGGCUGUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq new file mode 100644 index 0000000..f821f70 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.canicula.seq @@ -0,0 +1,2 @@ +>d.5.e.S.canicula +GCCUACGGCCAUACUAGUCUGAAAACGCCCGAUCUCGUCUGAUCUCGGAAGCUAAGCAGAUUCAGGCCUGGUUAGUACUUGGAUGGGAGACCGCCUGGGAAUACCAGGUGCAGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq new file mode 100644 index 0000000..99153a7 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cerevisiae.seq @@ -0,0 +1,2 @@ +>d.5.e.S.cerevisiae +GGUUGCGGCCAUAUCUACCAGAAAGCACCGUUUCCCGUCCGAUCAACUGUGUUAAGCUGGUAGAGCCUGACCGAGUAGUGUAUGGGUGACCAUACGCGAAACUCAGGUGCUGCAAUCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq new file mode 100644 index 0000000..7301bd3 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.cynthia.XBM.seq @@ -0,0 +1,2 @@ +>d.5.e.S.cynthia.XBM +GCCAACGUCCAUACCAUGUUGAAUACACCGGUUCUCGUCCGAUCACCGAAGUCAAGCAACAUCGGGCGUAGUCAGUACUUGGAUGGGUGACCGCCUGGGAACACUACGUGAUGUUGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq new file mode 100644 index 0000000..c309c20 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.kowalevskii.seq @@ -0,0 +1,2 @@ +>d.5.e.S.kowalevskii +GCCUACGGCCAUACCACGUAGAAUGCACCGGUUCUCGUCCGAUCACCGAAGUUAAGCUGCGUCGGGCGUGGUUAGUACUUGCAUGGGAGACCGGCUGGGAAUACCACGUGCUGUAGGCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq new file mode 100644 index 0000000..fbcd514 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.officinalis.seq @@ -0,0 +1,2 @@ +>d.5.e.S.officinalis +GCUUACGGCCAUAUCACGCUGAAAACACCGGUUCUCGUCCGAACACCGAAGUUAAGCAACGUAGAGCCUGGUGAGUACUUGGAUGGGUGACCGCUUGGGAAUACCAGGUGCUGUAAGCAU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq new file mode 100644 index 0000000..45e16c8 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.S.pombe.1.seq @@ -0,0 +1,2 @@ +>d.5.e.S.pombe.1 +GUCUACGGCCAUACCUAGGCGAAAACACCAGUUCCCGUCCGAUCACUGCAGUUAAGCGUCUGAGGGCCUCGUUAGUACUAUGGUUGGAGACAACAUGGGAAUCCGGGGUGCUGUAGGCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq new file mode 100644 index 0000000..dacd0d4 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.aestivum.seq @@ -0,0 +1,2 @@ +>d.5.e.T.aestivum +GGAUGCGAUCAUACCAGCACUAAGGCAUCGGAUCCCGUCAGAACUCCGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACAAGGAUGGGUGACCUCUUGGGAAGUCCUCGUGUUGCAUUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq new file mode 100644 index 0000000..91d76b6 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.borreli.seq @@ -0,0 +1,2 @@ +>d.5.e.T.borreli +GGGUACGUCCAUACUUGGCUGAAAGCACCAUAUCCCGUCCGAUUUGUGAAGUUAAGCAGCCACAGGCUUAGUUAGUACUGAGGUCAGUGAUGACUUGGGAACCCUAAGUGUCGUACUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq new file mode 100644 index 0000000..b4fe443 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.cruzi.seq @@ -0,0 +1,2 @@ +>d.5.e.T.cruzi +GGGUACGACCAUACUUGGCCGAGUGCACCACAUCCCGUCCGAUUUGUGAAGUUAAGCGGCCACAGGCCUCGUUAGUACGGCGAUCAGUGAUGGCGCUGGAACCCGGGGUGCCGUACCCUU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq new file mode 100644 index 0000000..0d095ee --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.monococcum.seq @@ -0,0 +1,2 @@ +>d.5.e.T.monococcum +GGAUGCGAUCAUACCAGCACUAAAGCACCGGAUCCCAUCAGAACUCUGAAGUUAAGCGUGCUUGGGCGAGAGUAGUACUAGGAUGGGUGACCUCCUCGGAAGUCCUCGUGUUGCAUUCCC diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq new file mode 100644 index 0000000..2846ec9 --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.T.thermophila.2.seq @@ -0,0 +1,2 @@ +>d.5.e.T.thermophila.2 +GUUGUCGGCCAUACUAAGGUGAAAACACCGGAUCCCAUUCGAACUCCGAAGUUAAGCGCCUUAAGGCUGGGUUAGUACUAAGGUGGGGGACCGCUUGGGAAGUCCCAGUGUCGAUAGCCU diff --git a/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq b/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq new file mode 100644 index 0000000..5b30dba --- /dev/null +++ b/gtfold-mfe/tests/data/5S_sequences/d.5.e.U.unicinctus.seq @@ -0,0 +1,2 @@ +>d.5.e.U.unicinctus +GUCUACGGCCAUACCACGUUGAAAACACCAGUUCUCGUCCGAUCACUGAAGUUAAGCAACGUCGGGCCCGGUUAGUACUUGGAUGGGUGACCGCCUGGGAAUACCGGGUGCUGUAGACUU diff --git a/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq b/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq new file mode 100644 index 0000000..2b55c97 --- /dev/null +++ b/gtfold-mfe/tests/data/constraints_sequences/combseq3.seq @@ -0,0 +1 @@ +CCCCAAAAGGGGAAAACCCCAAAAGGGGAAAACCCCAAAAGGGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.constraint new file mode 100644 index 0000000..7029d7d --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.constraint @@ -0,0 +1 @@ +F 1 8 8 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.seq new file mode 100644 index 0000000..0984ecd --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance1.seq @@ -0,0 +1 @@ +CCCCCGGGGGGAAAGGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.constraint new file mode 100644 index 0000000..adb4fdb --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.constraint @@ -0,0 +1,5 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 +F 24 25 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.seq b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.seq new file mode 100644 index 0000000..9a1d7d8 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/base_pair_distance2.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGGCCCACGAAAA diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult new file mode 100644 index 0000000..573541a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/default.expectedresult @@ -0,0 +1 @@ +0 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.constraint new file mode 100644 index 0000000..cece32a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 18 1 +F 4 7 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/duplicate_base1.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.constraint new file mode 100644 index 0000000..2ce893a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.constraint @@ -0,0 +1,4 @@ +F 0 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number1.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.constraint new file mode 100644 index 0000000..65ea20f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 24 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.seq b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/invalid_base_number2.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.constraint new file mode 100644 index 0000000..2a01386 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.constraint @@ -0,0 +1,4 @@ +F 1 19 2 +F 3 10 1 +F 4 8 1 +F 11 15 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.expectedresult new file mode 100644 index 0000000..573541a --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.expectedresult @@ -0,0 +1 @@ +0 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.seq new file mode 100644 index 0000000..0964dc3 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/normal_struct1.seq @@ -0,0 +1 @@ +CCCCAAGAAGCAAAGAAGG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.constraint new file mode 100644 index 0000000..2a8e728 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.constraint @@ -0,0 +1,2 @@ +F 1 19 2 +F 15 21 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.seq b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.seq new file mode 100644 index 0000000..23023c5 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot1.seq @@ -0,0 +1 @@ +CCAAAAAAAAAAAACAAGGAG diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.constraint b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.constraint new file mode 100644 index 0000000..bcbe409 --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.constraint @@ -0,0 +1,3 @@ +F 1 19 2 +F 3 10 2 +F 15 23 1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.expectedresult b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.expectedresult new file mode 100644 index 0000000..d00491f --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.expectedresult @@ -0,0 +1 @@ +1 diff --git a/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.seq b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.seq new file mode 100644 index 0000000..6b590de --- /dev/null +++ b/gtfold-mfe/tests/data/exitcodes_sequences/pseudoknot2.seq @@ -0,0 +1 @@ +CCCCAAAAGGAAAACAAGGAAAG diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq.seq new file mode 100644 index 0000000..ac737d0 --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/combseq.seq @@ -0,0 +1 @@ +CCCAAAAGGGAAAACCCAAAAGGG diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq new file mode 100644 index 0000000..2b55c97 --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/combseq3.seq @@ -0,0 +1 @@ +CCCCAAAAGGGGAAAACCCCAAAAGGGGAAAACCCCAAAAGGGG diff --git a/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq b/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq new file mode 100644 index 0000000..c2722ec --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/combseq4.seq @@ -0,0 +1 @@ +CCCCAAAACCCCAAAAGGGGAAAAGGGG diff --git a/gtfold-mfe/tests/data/subopt_sequences/cs1.seq b/gtfold-mfe/tests/data/subopt_sequences/cs1.seq new file mode 100644 index 0000000..5e4009c --- /dev/null +++ b/gtfold-mfe/tests/data/subopt_sequences/cs1.seq @@ -0,0 +1 @@ +CAAAAGAAAACAAAAG diff --git a/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm b/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm new file mode 100755 index 0000000..ddabcdc --- /dev/null +++ b/gtfold-mfe/tests/scripts/CompareGTCTwithUNACT.pm @@ -0,0 +1,64 @@ +#!/usr/bin/perl +package CompareGTCTwithUNACT; +use strict; +use warnings; +use Error; +use File::Basename; +use Exception::Class; + +require "compare_ct.pl"; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my $logger = $_[4]; + + my $epsilon = 0.001; + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + + while (($key, $value) = each(%Sequences)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $gtout = "$workdir$seqname-gt"; + my $unaout = "$workdir$seqname-una"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + my $unaoutfilename = $workdir."$seqname-una.ct"; + + my $gtcmd = "$gtdir/gtfold -m $seqfile --unafold -o $gtout > /dev/null"; + my $unacmd = "$unadir/hybrid-ss-min -s DAT $seqfile -o $unaout > /dev/null"; + + system("$gtcmd"); + system("$unacmd"); + + my @result; + eval { + @result = compare_ct_structures($gtoutfilename, $unaoutfilename); + }; + my $exception; + if ($exception = Exception::Class->caught('CompareCTException')) { + $logger->error("Test Failed: $seqname: $exception\n"); + next; + } + + my $diff1 = abs(1 - $result[0]); + my $diff2 = abs(1 - $result[1]); + if ($diff1 < $epsilon || $diff2 < $epsilon) { + $logger->info("TEST PASSED: $seqname: Specificity = $result[0], Selectivity = $result[1]"); + } + else { + $logger->info("TEST FAILED: $seqname: Specificity = $result[0], Selectivity = $result[1]\n". + "More Information: $result[2] $result[3]"); + } + } +} +1; diff --git a/gtfold-mfe/tests/scripts/ConstraintsVerification.pm b/gtfold-mfe/tests/scripts/ConstraintsVerification.pm new file mode 100755 index 0000000..22617bb --- /dev/null +++ b/gtfold-mfe/tests/scripts/ConstraintsVerification.pm @@ -0,0 +1,162 @@ +#!/usr/bin/perl +package ConstraintsVerification; +use strict; +use warnings; +use File::Basename; + +require 'test_utils.pl'; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + my %new_hash = (%local_sequences, %Sequences); + + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $dirname = dirname($seqfile); + my $constraint_file = "$workdir/$seqname.constraint"; + my $gtout = "$workdir$seqname-gt"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + + my $gtcmd; + $gtcmd = "$gtdir/gtfold $seqfile -o $gtout > /dev/null 2>&1"; + system("$gtcmd"); + my $len = get_seq_len_from_ctfile($gtoutfilename); + my $CONSFILE; + open($CONSFILE, '>', $constraint_file) or die "Couldn't open $_"; + generate_constraints(1, $len, $CONSFILE); + close $CONSFILE; + + my $gtout_constraints = $gtout."_constraints"; + my $gtout_constraints_filename = "$gtout_constraints.ct"; + $gtcmd = "$gtdir/gtfold -c $constraint_file $seqfile -o $gtout_constraints > /dev/null 2>&1"; + my $exitcode = system("$gtcmd") >> 8; + + if ($exitcode != 0) { + $logger->error("TEST FAILED: $seqname : Assertion Failed, Exit Code incorrect: $exitcode. Constraint File: $constraint_file"); + next; + } + + my @violated_constraints = verify_constraints($gtout_constraints_filename, $constraint_file); + if (@violated_constraints) { + my @vc = join(',', @violated_constraints); + print scalar(@violated_constraints); + $logger->error("TEST FAILED: $seqname : Constraints Violated: Input Constraint File $constraint_file. Violated Constraints:\n @vc"); + } + else { + $logger->info("TEST PASSED: $seqname : Input Constraint File $constraint_file"); + } + } +} + +sub generate_constraints +{ + my $i = shift; + my $j = shift; + my $CONSFILE = shift; + + return if ($j-$i< 4); + + my $r = rand(); + print $CONSFILE "F $i $j 1\n" if $r <0.4; + print $CONSFILE "P $i $j 1\n" if $r >0.4 && $r<0.8; + print $CONSFILE "P $i 0 1\n" if $r >0.8; + + my $range = $j-$i; + my $ii = int(rand($range)) + $i; + $range = $j-$ii; + my $jj = int(rand($range)) + $ii; + + generate_constraints($i+1,$ii-1, $CONSFILE); + generate_constraints($jj+1,$j-1, $CONSFILE); +} + +sub get_seq_len_from_ctfile +{ + my $filename = shift; + open(IN, "<$filename"); + my $header = ; # ignore first line + close IN; + my ($len, $dG) = split(' ', $header); + return $len; +} + +sub verify_constraints { + + my $ctfilename = shift; + my $cffilename = shift; + + open CT, $ctfilename; + open CF, $cffilename; + + my %ct_hash = (); + my @rna; + my $count=1; + + my $header = ; # ignore first line + while () + { + my @ff = split(' ', $_); + $ct_hash{$ff[0]} = $ff[4]; + $rna[$count] = $ff[1]; + ++$count; + } + + my @violated_constraints = (); + while() + { + chomp; + my @ff = split(' ', $_); + if ($ff[0] eq 'P' && $ff[2] == 0) { # case SS + if ($ct_hash{$ff[1]} != 0) { + print $_."\n"; + push(@violated_constraints, $_); + } + } + elsif ($ff[0] eq 'P' && $ct_hash{$ff[1]} == $ff[2] && $ct_hash{$ff[2]} == $ff[1]) { # case P + print $_."\n"; + print "$ct_hash{$ff[1]} $ct_hash{$ff[2]}\n"; + push(@violated_constraints, $_); + } + elsif ($ff[0] eq 'F' && $ff[2] == 0) { + my $b = canPair($rna[$ff[1]], $rna[$ff[2]]); + if ($b == 1) { + print $_."\n"; + push(@violated_constraints, $_); + } + } + } + + close CT; + close CF; + + return @violated_constraints; +} + +sub canPair { + my ( $i, $j) = @_; + # (A,U), (U,A), (C,G), (G,C), (G,U) and (U,G). + return 1 if ($i eq 'A' && $j eq 'U') ; + return 1 if ($i eq 'U' && $j eq 'A') ; + return 1 if ($i eq 'C' && $j eq 'G') ; + return 1 if ($i eq 'G' && $j eq 'C') ; + return 1 if ($i eq 'G' && $j eq 'U') ; + return 1 if ($i eq 'U' && $j eq 'G') ; + return 0; +} +1; diff --git a/gtfold-mfe/tests/scripts/ExitCodes.pm b/gtfold-mfe/tests/scripts/ExitCodes.pm new file mode 100755 index 0000000..fbe7079 --- /dev/null +++ b/gtfold-mfe/tests/scripts/ExitCodes.pm @@ -0,0 +1,62 @@ +#!/usr/bin/perl +package ExitCodes; +use strict; +use warnings; +use File::Basename; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + my %new_hash = (%local_sequences, %Sequences); + # For testing pseudoknot detection logic + # we may only test the sequences specified in local_sequences + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $dirname = dirname($seqfile); + my $constraint_file = "$dirname/$seqname.constraint"; + my $gtout = "$workdir$seqname-gt"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + + my $gtcmd; + if (-e $constraint_file) { + $gtcmd = "$gtdir/gtfold -c $constraint_file -m $seqfile -o $gtout > /dev/null 2>&1"; + } + else { + $gtcmd = "$gtdir/gtfold -m $seqfile -o $gtout > /dev/null 2>&1"; + } + + my $x = system("$gtcmd") >> 8; + + my $expected_result_file = "$dirname/$seqname.expectedresult"; + my $expected_result; + if (-e $expected_result_file) { + $expected_result = `head -n 1 $expected_result_file`; + } + else { + $expected_result = 0; + } + + if ($expected_result =~ $x) { + $logger->info("TEST PASSED: $seqname: Return Value $x matched expected output $expected_result"); + } + else { + $logger->error("TEST FAILED: $seqname: Return Value $x did not match expected output $expected_result"); + } + } +} +1; diff --git a/gtfold-mfe/tests/scripts/SampleTest.pm b/gtfold-mfe/tests/scripts/SampleTest.pm new file mode 100755 index 0000000..9686997 --- /dev/null +++ b/gtfold-mfe/tests/scripts/SampleTest.pm @@ -0,0 +1,26 @@ +#!/usr/bin/perl +package SampleTest; +use strict; +use warnings; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + my %new_hash = (%local_sequences, %Sequences); + + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + } +} +1; diff --git a/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm new file mode 100755 index 0000000..7cdfb82 --- /dev/null +++ b/gtfold-mfe/tests/scripts/Scoregtwithunafold.pm @@ -0,0 +1,60 @@ +#!/usr/bin/perl +package Scoregtwithunafold; +use strict; +use warnings; +use File::Basename; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $unadir = $Config{"G_UNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + + my $key; + my $value; + + while (($key, $value) = each(%Sequences)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $gtout = "$workdir$seqname-gt"; + my $unaout = "$workdir$seqname-una"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + my $unaoutfilename = $workdir."$seqname-una.ct"; + + my $gtcmd = "$gtdir/gtfold -m $seqfile --unafold -o $gtout > /dev/null"; + my $unacmd = "$unadir/hybrid-ss-min -s DAT $seqfile -o $unaout > /dev/null"; + + system("$gtcmd"); + system("$unacmd"); + my $gtfold_energy = `head -1 $gtoutfilename`; + my $unafold_energy = `head -1 $unaoutfilename`; + + if ($gtfold_energy =~ m/([0-9.-]+$)/) { + $gtfold_energy = $1; + } + if ($unafold_energy =~ m/dG = ([0-9.-]+)/) { + $unafold_energy = $1; + } + + if ($gtfold_energy eq $unafold_energy) { + $logger->info("TEST PASSED: $seqname: Energy Value matched for MFE -> $gtfold_energy"); + } + else { + $logger->error("TEST FAILED: $seqname: Energy Value Not Matched for MFE -> gtfold = $gtfold_energy, unafold = $unafold_energy"); + } + #my $ctcmd1 = "/usr/local/bin/ct-energy $gtoutfilename"; + #my $ctcmd2 = "/usr/local/bin/ct-energy -s DAT $unaoutfilename"; + #system("$ctcmd1"); + #print "ct-energy = "; + #system("$ctcmd2"); + } +} +1; diff --git a/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm new file mode 100755 index 0000000..fa9d7ed --- /dev/null +++ b/gtfold-mfe/tests/scripts/SuboptMatchStructures.pm @@ -0,0 +1,126 @@ +#!/usr/bin/perl +package SuboptMatchStructures; +use strict; +use warnings; +use File::Basename; + +sub test() +{ + my(%Config) = %{$_[1]}; + my(%Sequences) = %{$_[2]}; + my(%local_sequences) = %{$_[3]}; + my $logger = $_[4]; + + my $gtdir = $Config{"G_GTFOLD_DIR"}; + my $rnadir = $Config{"G_RNAFOLD_DIR"}; + my $workdir = $Config{"G_WORK_DIR"}; + my $min_energy = $Config{"L_SUBOPTMATCHSTRUCTURES_MIN_ENERGY"}; + my $max_energy = $Config{"L_SUBOPTMATCHSTRUCTURES_MAX_ENERGY"}; + my $energy_stride = $Config{"L_SUBOPTMATCHSTRUCTURES_ENERGY_STRIDE"}; + + if (not(defined($min_energy))) { + $min_energy = 0; + } + if (not(defined($max_energy))) { + $max_energy = 3; + } + if (not(defined($energy_stride))) { + $energy_stride = 1; + } + + my $key; + my $value; + my %new_hash = (%local_sequences); + + while (($key, $value) = each(%new_hash)) { + + my $seqname=$key; + my $path; + my $suffix; + + my $seqfile = $value; + my $dirname = dirname($seqfile); + my $gtout = "$workdir$seqname-gt"; + my $rnaout = "$workdir$seqname-rna"; + my $gtoutfilename = $workdir."$seqname-gt.ct"; + + my %gtstruct_hash; + my %rnastruct_hash; + + my $energy; + for ($energy=$min_energy; $energy<=$max_energy; $energy=$energy+$energy_stride) { + + my $gtfile = $gtout.$energy; + my $rnafile = $rnaout.$energy."_ss.txt"; + my $gtcmd; + my $rnacmd; + $gtcmd = "$gtdir/gtfold --subopt $energy $seqfile -o $gtfile > /dev/null 2>&1"; + $rnacmd = "$rnadir/RNAsubopt -s DAT -e $energy < $seqfile > $rnafile"; + + system("$gtcmd"); + system("$rnacmd"); + + my $gtsubopt_file = $gtfile."_ss.txt"; + my $rnasubopt_file = $rnafile; + + my $gtsorted = $gtsubopt_file."_sorted"; + my $rnasubopt_sorted = $rnafile."_sorted"; + my $gtstructs = `cat $gtsubopt_file | sed '/[A-Z]/d' | sed '/^\$/d'`; + my $rnastructs = `cat $rnasubopt_file | sed '/[A-Z]/d' | sed '/^\$/d'`; + + %gtstruct_hash = split('[ \n]',$gtstructs); + %rnastruct_hash = split('[ \n]',$rnastructs); + + my $diff_file_name = "$workdir$seqname\_$energy.diff"; + + open (DIFF_FILE, ">> $diff_file_name"); + + my $diff = 0; + foreach my $key ( keys %gtstruct_hash ) + { + my $change = $gtstruct_hash{$key} + unless ( (exists $rnastruct_hash{$key}) && $gtstruct_hash{$key} eq $rnastruct_hash{$key} ); + # gotta check for existence to quiet warnings. + if(defined($change) && $change ne "") { + print DIFF_FILE $key. "\nGTFOLD Energy: ". $gtstruct_hash{$key}; + if (exists $rnastruct_hash{$key}) { + print DIFF_FILE "\nRNASubopt Energy: ". $rnastruct_hash{$key}; + } + else { + print DIFF_FILE "\nRNASubopt Energy: No corresponding structure"; + } + print DIFF_FILE "\n"; + $diff = 1; + } + } + + foreach my $key ( keys %rnastruct_hash ) + { + my $change = $rnastruct_hash{$key} + unless ( (exists $gtstruct_hash{$key}) && $gtstruct_hash{$key} eq $rnastruct_hash{$key} ); + # gotta check for existence to quiet warnings. + if(defined($change) && $change ne "") { + print DIFF_FILE $key. "\nRNASubopt Energy: ". $rnastruct_hash{$key}; + if (exists $gtstruct_hash{$key}) { + print DIFF_FILE "\nGTFOLD Energy: ". $gtstruct_hash{$key}; + } + else { + print DIFF_FILE "\nGTFOLD Energy: No corresponding structure"; + } + print DIFF_FILE "\n"; + $diff = 1; + } + } + + close DIFF_FILE; + + if ($diff == 0) { + $logger->info("TEST PASSED: $seqname: energy delta = $energy: Suboptimal Structures matched"); + } + else { + $logger->error("TEST FAILED: $seqname: energy delta = $energy: Suboptimal Structures not matched. Difference Written to file $diff_file_name"); + } + } + } +} +1; diff --git a/gtfold-mfe/tests/scripts/compare_ct.pl b/gtfold-mfe/tests/scripts/compare_ct.pl new file mode 100755 index 0000000..7196ffe --- /dev/null +++ b/gtfold-mfe/tests/scripts/compare_ct.pl @@ -0,0 +1,339 @@ +#!/usr/bin/perl + +use paul_specials; +use Error; +use Exception::Class('CompareCTException'); + +sub compare_ct_structures() +{ +my $ref_filename=$_[0]; +my $filename=$_[1]; + +open(REF, "< $ref_filename"); +open(RNA, "< $filename"); + +#printf "opened files $ref_filename and $filename\n\n\n"; + +@ref_struct = read_struct_ct(*REF); +@struct = read_struct_ct(*RNA); + +my $rlen = length($ref_struct[0]); +my $slen = length($struct[0]); +my $ref_seq = $ref_struct[0]; +my $seq = $struct[0]; + +$ref_struct[0]=$rlen; +$struct[0]=$slen; + +my $ref_dotb = table_to_bracket(\@ref_struct); +my $dotb = table_to_bracket(\@struct); + +$dotb =~ s/\(/\{/g; +$dotb =~ s/\)/\}/g; + + $_ = $ref_seq; + my $ref_nogaps = tr/\-//; + $_ = $seq; + my $nogaps = tr/\-//; + + + if (($rlen-$ref_nogaps) != ($slen-$nogaps)){ + CompareCTException->throw(error => "seq lengths aren't equal (reference = $rlen, prediction = $slen)! +$rlen-$ref_nogaps ne $slen-$nogaps +ref_nogaps = $ref_nogaps +nogaps = $nogaps + +>ref +$ref_seq +$ref_dotb +>str +$seq\n\n\n"); + } + +#print ">ref1 +#$ref_seq +#$ref_dotb +#>str1 +#$seq +#$dotb\n\n\n"; + +#If different lengths, gap or delete as appropriate: +while ($rlen != $slen){ + + for (my $i = 0; $i < length($ref_seq); $i++){ + if ( substr($ref_seq,$i,1) =~ '\-'){ + + if (substr($ref_dotb,$i,1) =~ '\.' ){ + substr($ref_seq,$i,1) = ""; + substr($ref_dotb,$i,1) = ""; + $i--; + } + elsif ((substr($seq,$i,1) ne substr($ref_seq,$i,1)) && (substr($ref_dotb,$i,1) ne '\.') ) { + substr($seq,$i,0) = "."; + substr($dotb,$i,0) = "."; + + substr($ref_seq,$i,1) = "."; + + + } + } + } + + + for (my $i = 0; $i < length($seq); $i++){ + + if ( substr($seq,$i,1) =~ '\-'){ + + if (substr($dotb,$i,1) =~ '\.' ){ + substr($seq,$i,1) = ""; + substr($dotb,$i,1) = ""; + $i--; + } + elsif (substr($seq,$i,1) ne substr($ref_seq,$i,1) && (substr($dotb,$i,1) ne '\.')) { + substr($ref_seq,$i,0) = "."; + substr($ref_dotb,$i,0) = "."; + substr($seq,$i,1) = "."; + + } + } + + } +#print ">ref +#$ref_seq +#$ref_dotb +#>str +#$seq +#$dotb\n\n"; + @ref_struct = make_pair_table($ref_dotb); + @struct = make_pair_table($dotb); + + #Update lengths after gapping + $rlen = length($ref_seq); + $slen = length($seq); + +} + + + +#print ">ref +#$ref_seq +#$ref_dotb +#>str +#$seq\n"; + + + +my $rcount = 0; +my $scount = 0; +my $true_pos = 0; +my $true_neg = 0; +my $false_neg = 0; +my $false_pos = 0; +my $conflict = 0; +my $contradict = 0; +my $temp = 0; + +for (my $i=1; $i<=$rlen; $i++){ + + #printf "%6d %6d\n", $ref_struct[$i], $struct[$i]; + + if ($ref_struct[$i]>0 && $ref_struct[$i]>$i){ + $rcount++; + #print "$rcount: $i-$ref_struct[$i]\n"; + } + + if ($struct[$i]>0 && $struct[$i]>$i){ + $scount++; + } + + if (($ref_struct[$i]==$struct[$i]) && $ref_struct[$i]>0 && $ref_struct[$i]>$i){ + #printf "%6d %6d\n", $ref_struct[$i], $struct[$i]; + $true_pos++; + $temp = $struct[$i]; + substr($dotb,$i-1,1) = '('; + substr($dotb,$temp-1,1) = ')'; + } + elsif (($ref_struct[$i]!=$struct[$i]) && $struct[$i]>0 && $struct[$i]>$i){ + + #print "struct: $i . $struct[$i]\n"; + + $prime5 = $i; + $prime3 = $struct[$i]; + + if ($ref_struct[$prime3]>0 || $ref_struct[$prime5]>0){ + #print " ref: $ref_struct[$prime3] . $ref_struct[$ref_struct[$prime3]] : $ref_struct[$prime5] . $ref_struct[$ref_struct[$prime5]]\n"; + $contradict++; + + substr($dotb,$prime5-1,1) = '<'; + substr($dotb,$prime3-1,1) = '>'; + + + } + else { + #check nested! + $j=$prime5; + $b=1; + while ($b && $j<$prime3 ) { + + if ( ($ref_struct[$j]>0 && $ref_struct[$j]<$prime5) || $ref_struct[$j]>$prime3 ) { + $b=0; + $conflict++; + #print "conflict $ref_struct[$j] . $j\n"; + + substr($dotb,$prime5-1,1) = '['; + substr($dotb,$prime3-1,1) = ']'; + + } + $j++; + } + + } + + + } + + for (my $j=$i+4; $j<=$rlen; $j++){ + + my $x = substr($ref_seq,$i-1,1); + my $y = substr($ref_seq,$j-1,1); + + if (ispair($x,$y) ){ + $true_neg++; + #print "$x $i $y $j\n"; + } + + } + + +} + + +#$false_pos = $scount - $true_pos; +$false_pos = $conflict + $contradict; +$false_neg = $rcount - $true_pos; + +$true_neg=$true_neg-$true_pos-$false_pos; + +my $sensitivity = 0; +my $selectivity =0; +if ($rcount>0){ + $sensitivity = $true_pos/($false_neg + $true_pos); #$rcount; +} +if ($scount>0){ + $selectivity = $true_pos/($false_pos + $true_pos); #$scount; +} + +my $approx_corr = ($sensitivity + $selectivity)/2; +my $N = $true_pos + $false_pos + $false_neg + $true_neg; + +my $corr_coeff = 0; +if ($true_pos>0){ +$corr_coeff = ($N*$sensitivity*$selectivity - $true_pos)/sqrt(($N*$sensitivity - $true_pos)*($N*$selectivity - $true_pos)); +} + + +my $MCC = 0; +my $MCCquotient = (($true_pos+$false_pos)*($true_pos+$false_neg)*($true_neg+$false_pos)*($true_neg+$false_neg)); + +if ($MCCquotient>0){ +$MCC = ($true_pos*$true_neg - $false_pos*$false_neg)/sqrt( $MCCquotient ); +} + +$old_false_pos = $scount - $true_pos; +$compatable = $old_false_pos - $false_pos; + +#print ">ref +#$ref_seq +#$ref_dotb +#>str +#$seq\n"; +#print "$dotb\n"; + +my $comparison_result = " +seq length = %6d +num of bps in ref = %6d +num of bps in sub = %6d +Basepair distance = %6d +true positives = %6d +true negatives = %6d +false positive = %6d +\t contradict = $contradict +\t conflict = $conflict +\t compatable = $compatable +false negative = %6d +sensitivity = %1.3f +selectivity = %1.3f +Approximate correlation = %1.3f +Correlation Coefficient = %1.3f +Matthews Corr. Coeff. = %1.3f + +\n\n", $rlen, $rcount, $scount, $false_pos+$false_neg+$compatable, $true_pos, $true_neg, $false_pos, $false_neg, $sensitivity, $selectivity, $approx_corr, $corr_coeff, $MCC; + +my $latex_comparison_result = "LaTeX: +Subj. File & BPs in Ref. & BPs in Subj. & TPs (sens.)& FPs (select.) & Matthews Corr. Coeff. (approx. corr.) & \\\\ +$filename & %d & %d & %d (%2.1f) & %d (%2.1f) & %1.3f (%2.1f) \\\\ \n\n", +$rcount, $scount, $true_pos, $sensitivity*100, $false_pos, $selectivity*100, $MCC, $approx_corr*100; + +#printf "%1.4f\t%1.4f\n", +#$sensitivity, $selectivity; + + return ($sensitivity, $selectivity, $comparison_result, $latex_comparison_result); +} + +sub read_struct_ct{ + +$fileptr = $_[0]; +my $seq = ""; + +my $i=-1; +while ( <$fileptr> ){ + + @F = split; + + #if ((/ = /) && ($#F!=5)) { + # next; + #} + + if ($i>=0){ + + $seq .= $F[1]; + $table[$i] = $F[4]; +} + $i++; + + #if ($F[4]==0) {$s .= "."; next} + #$s .= "(" if ($F[0]<$F[4]); + #$s .= ")" if ($F[0]>$F[4]); +} + + + $seq =~ tr/a-z/A-Z/; +#print "2: $seq\n\n"; + +return ($seq, @table); + +} + +sub ispair{ + my ($x, $y) = @_; + + if ( ($x eq 'A' && $y eq 'U')||($x eq 'U' && $y eq 'A') ) { + + return 1; + } + elsif ( ($x eq 'G' && $y eq 'C')||($x eq 'C' && $y eq 'G') ) { + + return 1; + } + elsif ( ($x eq 'G' && $y eq 'U')||($x eq 'U' && $y eq 'G') ) { + + return 1; + } + + else { + return 0; + } +} + +# End of file +1; diff --git a/gtfold-mfe/tests/scripts/paul_specials.pm b/gtfold-mfe/tests/scripts/paul_specials.pm new file mode 100755 index 0000000..304260d --- /dev/null +++ b/gtfold-mfe/tests/scripts/paul_specials.pm @@ -0,0 +1,163 @@ +package paul_specials; + +use strict; +use warnings; + +require Exporter; +our @ISA = qw(Exporter); +our @EXPORT = qw( table_to_bracket table_to_bracket5 make_pair_table); + +#input is base-pair table, output is dot-bracket notation. NOte: $table[0]=seq_length. +#ADD PKNOTS SUPPORT! +sub table_to_bracket { + + my $ref = shift; + my $dotb = "."; + my $temp = 0; + + my @tbl = @$ref; # + my $len = $tbl[0]; + + for (my $j = 0; $j < $len; $j++ ) { + substr($dotb, $j, 1) = "."; + } + #print "\n$dotb\n\n"; + + for (my $j = 1; $j < $len+1; $j++ ) { + + if ($tbl[$j]>$j) { + substr($dotb, $j-1, 1) = "\("; + $temp = $tbl[$j] - 1; + substr($dotb, $temp, 1) = "\)"; + } + + } + + return $dotb; +} + +sub table_to_bracket5 { + + my $ref = shift; + my $dotb = "."; + my $temp = 0; + + my @tbl = @$ref; + my $len = $tbl[0]+1; + + #print "table_to_bracket: len = $len\n"; + + for (my $j = 0; $j < $len; $j++ ) { + substr($dotb, $j, 1) = "."; + } + + for (my $j = 0; $j < $len; $j++ ) { + + if ($tbl[$j+1]>$j+1) { + substr($dotb, $j, 1) = "\("; + $temp = $tbl[$j+1] - 2; + substr($dotb, $temp, 1) = "\)"; + } + #elsif ($tbl[$j+1]== 0) { + # substr($dotb, $j, 1) = "\."; + #} + } + + return $dotb; +} + + + +sub make_pair_table { + my $str = shift; + my $i; + my @bps = (); + my @bps_square = (); + my @bps_curly = (); + my @bps_angle = (); + my @pair_table; + my $prime5; + my $prime3; + my $count = 0; + + my $len = length($str); + + #print "make_pair_table: len = $len\n"; + + $pair_table[0] = $len; + + for (my $j = 0; $j < $len; $j++ ) { + $pair_table[$j+1] = 0; + if ( substr($str,$j,1) =~ '\(' ){ + push(@bps, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\)' ){ + $prime5 = pop(@bps); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + #print "base-pair: $pair_table[$i][$prime3] . $pair_table[$i][$prime5]\n" + } + elsif ( substr($str,$j,1) =~ '\[' ){ + push(@bps_square, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\]' ){ + $prime5 = pop(@bps_square); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + } + elsif ( substr($str,$j,1) =~ '\{' ){ + push(@bps_curly, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\}' ){ + $prime5 = pop(@bps_curly); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + } + elsif ( substr($str,$j,1) =~ '\<' ){ + push(@bps_angle, $j); + ++$count; + } + elsif ( substr($str,$j,1) =~ '\>' ){ + $prime5 = pop(@bps_angle); + $prime3 = $j; + $pair_table[$prime3+1] = $prime5+1; + $pair_table[$prime5+1] = $prime3+1; + --$count; + } + } + +#({[<.>]}) + +#print "pair table:\n"; +#for ($i = 1; $i < $len+1; $i++ ) { +# print "$pair_table[$i] "; +#} + +#print "\n"; +# +#print "pair_table = $#pair_table\n"; + +if ($count){ + print "Unbalanced brackets in: +$str\n"; + die; +} + + + return @pair_table; + +} + + + + +1; diff --git a/gtfold-mfe/tests/scripts/start_test.pm b/gtfold-mfe/tests/scripts/start_test.pm new file mode 100755 index 0000000..83fb8ee --- /dev/null +++ b/gtfold-mfe/tests/scripts/start_test.pm @@ -0,0 +1,130 @@ +#!/usr/bin/perl +use strict; +use warnings; +use Module::Load; + +use File::Basename; +use File::Path; +use Log::Log4perl qw(:easy); + +require 'test_utils.pl'; + +my $configdir="../config"; + +Log::Log4perl::init( "$configdir/root-logger.conf" ); +my $logger = Log::Log4perl->get_logger; + + +$logger->info("Starting Tests..."); + +# Read Parameter File +my $paramfile = "$configdir/test-params.conf"; + +# Create Work Directory +my $workdir = "../work"; +$logger->info("Deleting directory $workdir"); +rmtree($workdir, 0, 1); +$logger->info("Creating work directory $workdir"); +mkdir $workdir; + +my %Config; + +%Config = load_config_file($paramfile); + +###### Prepare a Hashmap of Sequences ###### + +my %Sequences; +my @seqdir_arr = @{$Config{"G_SEQUENCE_DIR"}}; + +my $seq_include_regex = $Config{"G_INCLUDE_SEQUENCES"}; +my $seq_exclude_regex = $Config{"G_EXCLUDE_SEQUENCES"}; + +%Sequences = find_sequences_from_dir( + seq_include_regex => $seq_include_regex, + seq_exclude_regex => $seq_exclude_regex, + seq_dirs => @seqdir_arr); + +my $test_include_regex = $Config{"G_INCLUDE_TESTS"}; +my $test_exclude_regex = $Config{"G_EXCLUDE_TESTS"}; + +my $test_list_file = $Config{"G_TEST_LIST_FILE"}; + +open(TESTLISTFILE, $test_list_file) || die("Could not open file: $test_list_file"); + + while () { + + my $testname = $_; + chomp($testname); + + $testname =~ s/^\s*//; # Remove spaces at the start of the line + $testname =~ s/\s*$//; # Remove spaces at the end of the line + if ( ($testname !~ /^#/) && ($testname ne "") ) { # Ignore lines starting with # and blank lines + + my $test_include = (not defined($test_include_regex)) || ($testname =~ /$seq_include_regex/); + my $test_exclude = (not defined($test_exclude_regex)) || ($testname !~ /$test_exclude_regex/); + + if ( $test_include && $test_exclude ) { + my $uppertestname = uc($testname); + my $local_sequence_dirname = "L_".$uppertestname."_SEQUENCE_DIR"; + my $local_sequence_include_regex = $Config{"L_".$uppertestname."_SEQUENCE_INCLUDE"}; + my $local_sequence_exclude_regex = $Config{"L_".$uppertestname."_SEQUENCE_EXCLUDE"}; + my @local_sequence_dir; + my %local_sequences; + + if (defined($Config{$local_sequence_dirname})) { + @local_sequence_dir = @{$Config{$local_sequence_dirname}}; + %local_sequences = find_sequences_from_dir( + seq_include_regex => $local_sequence_include_regex, + seq_exclude_regex => $local_sequence_exclude_regex, + seq_dirs => @local_sequence_dir); + } + + my $module = $testname; + load($module); + $module->test(\%Config, \%Sequences, \%local_sequences, $logger); + } + } + } + + +sub find_sequences_from_dir +{ + +my %args = @_; + +my %seq_hash; +my $include_regex = $args{seq_include_regex}; +my $exclude_regex = $args{seq_exclude_regex}; +my @seqdirs = $args{seq_dirs}; + +if (scalar(@seqdirs) eq 0) { + return %seq_hash; +} + +foreach (@seqdirs) { + + opendir(DIR, $_) || die $!; + while (my $seqfile = readdir(DIR)) { + + my $seqname; + my $path; + my $suffix; + ($seqname,$path,$suffix) = fileparse($seqfile, (".seq", ".constraint")); + + if ((-d $seqfile) || $suffix ne '.seq') { + next; + } + + $seqfile = "$_$seqname$suffix"; + my $seq_include = (not defined($include_regex)) || ($seqname =~ /$include_regex/); + my $seq_exclude = (not defined($exclude_regex)) || ($seqname !~ /$exclude_regex/); + + if ( $seq_include && $seq_exclude ) { + $seq_hash{$seqname} = $seqfile; + $logger->info("Selected Sequence ... $seqname"); + } + } + +} + return %seq_hash; +} diff --git a/gtfold-mfe/tests/scripts/test_utils.pl b/gtfold-mfe/tests/scripts/test_utils.pl new file mode 100755 index 0000000..2a62542 --- /dev/null +++ b/gtfold-mfe/tests/scripts/test_utils.pl @@ -0,0 +1,84 @@ +#!/usr/bin/perl +use strict; +use File::Path; + +sub load_config_file() +{ + my $paramfile = $_[0]; + my %Config; + my $Name; + my $Value; + my $line; + my $orig_value; + open(PARAMFILE, $paramfile) || die("Could not open file: $paramfile"); + + while () { + + my $line = $_; + chomp($line); + + $line =~ s/^\s*//; # Remove spaces at the start of the line + $line =~ s/\s*$//; # Remove spaces at the end of the line + if ( ($line !~ /^#/) && ($line ne "") ) { # Ignore lines starting with # and blank lines + ($Name, $Value) = split (/=/, $line); # Split each line into name value pairs + + if ($Name =~ /.*_INCLUDE_SEQUENCES|.*_EXCLUDE_SEQUENCES|G_INCLUDE_TESTS|G_EXCLUDE_TESTS/) { + $orig_value= %Config->{$Name}; + $Value =~ s/[.]/\\./g; + $Value =~ s/[*]/.\*/g; + if ($orig_value ne "") { + $Value = $orig_value."|".$Value; + } + } + + if ($Name =~ /.*_SEQUENCE_DIR/) { + my @seqdir_arr = %Config->{$Name}; + push (@{%Config->{$Name}}, $Value); + next; + } + + %Config->{$Name} = $Value; # Create a hash of the name value pairs + + } + } + + $Value = %Config->{"G_INCLUDE_SEQUENCES"}; + +# printf($Value."\n"); +# if ("rad" =~ /\G$Value/) { +# printf("matched1\n"); +# } +# printf($Value."\n"); +# if ("a.a.dvdsf" =~ /\G(rad|a\..*)/g) { +# printf("matched2\n"); +# } +# printf($Value."\n"); +# if ("daf" =~ /\G$Value/) { +# printf("matched3\n"); +# } +# printf($Value."\n"); +# if ("d.afdsf" =~ /\G$Value/) { +# printf("matched4\n"); +# } +# printf($Value."\n"); +# if ("acc1" =~ /\G$Value/) { +# printf("matched5\n"); +# } +# printf($Value."\n"); +# if ("acc11" =~ /\G$Value/) { +# printf("matched6\n"); +# } +# printf($Value."\n"); +# if ("a..afjlhfj" =~ /\G$Value/) { +# printf("matched7\n"); +# } +# printf($Value."\n"); +# if ("afdjs" =~ /\G$Value/) { +# printf("matched8\n"); +# } + +# printf ("@{%Config->{'G_SEQUENCE_DIR'}}\n"); + + return %Config; +} +1;