cblaster v1.4

This release resolves some long standing bugs and adds support for searching against the ClusteredNR database.

What's Changed

• Initial support for searches against the ClusteredNR database (NR database clustered at 90% identity). To enable, specify nr_cluster_seq as a database when performing remote mode searches, e.g.: cblaster search -qf query.fasta -m remote -db nr_cluster_seq. This should give significantly faster remote searches compared to the regular NR database (which remains the default). Note that query sequences are only searched against NR cluster representative sequences; clusters are then expanded to include other sequences in the cluster, and hit data (identity, coverage, evalue, bitscore) for all member sequences are taken from the representative hit.
• Don't add empty sequences to DB so diamond does not fail by @biobeni in #122
• Fix GenBank parsing when first gene wraps chromosome start/end by @biobeni in #121
• Fix missing database and empty .fasta file error by @kaileyhh in #111
• Lowered default hitlist size to 500 to avoid BLAST result errors
• Fixed search bug caused by query sequence headers containing whitespace

New Contributors

• @biobeni made their first contribution in #122
• @kaileyhh made their first contribution in #111

Full Changelog: v1.3.20...v1.4

cblaster v1.3.20

What's Changed

• fix(remote): accommodated change in NCBI API by @FriederikeBiermann in #115

New Contributors

• @FriederikeBiermann made their first contribution in #115

Full Changelog: v1.3.19...v1.3.20

cblaster v1.3.19

What's Changed

• Checks for mistranslations in CDS annotations and truncated regions, other minor changes by @malanjary-wur in #94
• Update CITATION.cff with paper DOI by @althonos in #106

New Contributors

• @althonos made their first contribution in #106

Full Changelog: v1.3.18...v1.3.19

cblaster v1.3.18

• Fix NoneType error during result formatting (#90)
• Some bug fixes for stability (#87)

cblaster v1.3.17

• Fix off-by-one issues in extract_clusters module with intermediate genes (#83)
• Check for empty fields in IPG table (#85)

cblaster v1.3.16

• Fixes broken identical protein groups efetch request by setting db=ipg instead of db=protein (#84)
• Convert coordinates from IPG table to zero-based

cblaster v1.3.15

• Catch ValueError when parsing GFF sequence-region directive without coordinates
• Do not install genomicsqlite if installing cblaster on arm64

cblaster v1.3.14

• Fall back to built-in sqlite3 module when importing genomicsqlite fails

cblaster v1.3.13

Thanks to @brymerr921:

Bug fixes:

• By default, diamond blastp only saves a maximum of 25 hits per query, severely limiting the number of blast hits reported. Large databases are especially impacted. To solve this, the --hitlist_size is now passed on diamond inside cblaster search -m local. (1c16caa) (See issue #75)
• Added an option to cblaster makedb allowing users to provide a single txt file containing a list of input files. This solves the issue where the operating system limits the length of wildcard expansion on the command line. (bb9085c)
• Fixed error that arose when specifying sum or max for -bkey (fee315e) (see issue #76, thanks to @chasemc)

Enhancements:

• diamond makedb now uses the number of CPUs requested by the user (instead of all available CPUs) (0db55cc)

File compression:

• Use genomcsqlite3 to reduce the size of the final sqlite3 database by 40-60% (bae6b31)
• cblaster makedb accepts gzipped input files (241894d)
• cblaster makedb now writes a fasta.gz output file (241894d) and informs users they will need to decompress first if running hmmsearch (4c63fa5)

cblaster v1.3.12

• Fix extract_clusters module not working for HMM searches (2dcae87)