[WIP] Add tests for the cli

.gitignore

@@ -1,4 +1,5 @@
 *.pyc
+.cache
 birdy.egg-info
 birdy.log
 build

.travis.yml

@@ -0,0 +1,13 @@
+language: python
+python:
+  - "3.5"
+env:
+  - TOX_ENV=flake8
+  - TOX_ENV=py27
+  - TOX_ENV=py33
+  - TOX_ENV=py34
+  - TOX_ENV=py35
+install:
+  - pip install tox
+script:
+- tox -e $TOX_ENV

MANIFEST.in

@@ -0,0 +1,7 @@
+include LICENCE
+include README.md
+include requirements.txt
+include requirements-dev.txt
+include tox.ini
+recursive-include tests *
+recursive-include scripts *

Makefile

@@ -0,0 +1,20 @@
+# Birdy
+
+all: install
+
+install:
+	python setup.py install
+
+install-dev:
+	pip install -r requirements-dev.txt
+	python setup.py develop
+
+clean:
+	find . -name '*.pyc' -delete
+	find . -name '__pycache__' -type d | xargs rm -fr
+
+distclean: clean
+	rm -fr *.egg *.egg-info/
+
+test:
+	venv/bin/py.test -vs tests/

birdy/compat.py

@@ -0,0 +1,21 @@
+"""
+Python2/3 compatibility library
+"""
+import os
+
+
+def makedirs(path, exist_ok=False):
+    """Compatibility layer for os.makedirs"""
+    # Python 3
+    try:
+        os.makedirs(path, exist_ok=exist_ok)
+    except TypeError:
+        # Python 2
+        try:
+            os.makedirs(path)
+        except OSError as e:
+            # We do not care if the directory already exists
+            if e.errno == 17 and exist_ok is True:
+                pass
+            else:
+                raise

birdy/config.py

@@ -44,7 +44,7 @@
 DSSP_ID_URL = 'ftp://' + DSSP_FTP_HOST + DSSP_FTP_PATH + '{id}.dssp'
 
 # -- InterProScan
-INTERPRO_IDS_URL = 'ftp://ftp.ebi.ac.uk/pub/databases/interpro/Current/interpro.xml.gz'  # NOPEP8
+INTERPRO_IDS_URL = 'ftp://ftp.ebi.ac.uk/pub/databases/interpro/current/interpro.xml.gz'  # NOPEP8
 INTERPRO_ID_URL = 'http://www.ebi.ac.uk/interpro/entry/{id}/proteins-matched?export={fmt}'  # NOPEP8
 INTERPRO_MAX_PROTEIN_COUNT = 50
 

birdy/converter/clustal.py

@@ -30,13 +30,13 @@ def generate_clustal_set(output_path, formats, input_ids=None, use_cache=True):
             use_cache=use_cache
         )
 
-        alignements = []
+        alignments = []
         for ipro in output_files:
-            alignements += [clustalw(ipro)]
+            alignments += [clustalw(ipro)]
         logging.info(
-            "{} files have been aligned with clustalw".format(len(alignements))
+            "{} files have been aligned with clustalw".format(len(alignments))
         )
 
     logging.info("CLUSTAL | Execution time was {:.3f} s".format(t.secs))
 
-    return alignements
+    return alignments

birdy/fetcher/dssp.py

@@ -1,11 +1,12 @@
 import logging
 import os.path
 import sys
-import urllib.request
 
 from ftplib import FTP
+from six.moves.urllib import request
 
 from .. import config
+from ..compat import makedirs
 from ..utils import get_random_ids, Timer
 
 
@@ -32,7 +33,7 @@ def get_dssp_ids(use_cache=True):
         logging.info("Updating DSSP ids cache...")
 
         # Create cache directory if it does not exists
-        os.makedirs(config.IDS_LIST_CACHE_ROOT, exist_ok=True)
+        makedirs(config.IDS_LIST_CACHE_ROOT, exist_ok=True)
 
         # Fetch ids
         ftp = FTP(config.DSSP_FTP_HOST)
@@ -78,12 +79,12 @@ def fetch_dssp(ID, output_path='.'):
     fmt_path = os.path.join(output_path, fmt)
     output_file = os.path.join(fmt_path, filename)
 
-    os.makedirs(fmt_path, exist_ok=True)
+    makedirs(fmt_path, exist_ok=True)
 
     url = config.DSSP_ID_URL.format(id=ID)
 
     try:
-        urllib.request.urlretrieve(url, output_file)
+        request.urlretrieve(url, output_file)
     except:
         logging.error(
             "Cannot fetch id {id} from the CMBI. "

birdy/fetcher/interpro.py

@@ -2,12 +2,13 @@
 import os
 import os.path
 import requests
-import urllib.request
 import xmltodict
 
 from gzip import GzipFile
+from six.moves.urllib import request
 
 from .. import config
+from ..compat import makedirs
 from ..exceptions import NetworkError
 from ..utils import get_random_ids, Timer
 
@@ -32,7 +33,7 @@ def get_interpro_ids(use_cache=True):
         logging.info("Updating interpro ids cache. This may take minutes...")
 
         # Create cache directory if it does not exists
-        os.makedirs(config.IDS_LIST_CACHE_ROOT, exist_ok=True)
+        makedirs(config.IDS_LIST_CACHE_ROOT, exist_ok=True)
 
         ids = []
 
@@ -56,7 +57,7 @@ def select_interpro_entries(path, item):
 
         # Attention, tricky part
         # We stream ftp response in a GzipFile that is streamed by xmltodict
-        with urllib.request.urlopen(config.INTERPRO_IDS_URL) as f:
+        with request.urlopen(config.INTERPRO_IDS_URL) as f:
             xmltodict.parse(
                 GzipFile(fileobj=f),
                 item_depth=2,
@@ -100,7 +101,7 @@ def fetch_interpro(ID, fmt='fasta', output_path='.'):
 
     output_file = os.path.join(output_path, filename)
 
-    os.makedirs(output_path, exist_ok=True)
+    makedirs(output_path, exist_ok=True)
 
     url = config.INTERPRO_ID_URL.format(id=ID, fmt=fmt)
 

birdy/fetcher/kegg.py

@@ -3,6 +3,7 @@
 import requests
 
 from .. import config
+from ..compat import makedirs
 from ..exceptions import NetworkError
 from ..utils import get_random_ids, Timer
 
@@ -32,7 +33,7 @@ def get_kegg_ids(db, use_cache=True):
         logging.info("Updating KEGG ids cache for {} database...".format(db))
 
         # Create cache directory if it does not exists
-        os.makedirs(config.KEGG_IDS_LIST_CACHE_ROOT, exist_ok=True)
+        makedirs(config.KEGG_IDS_LIST_CACHE_ROOT, exist_ok=True)
 
         url = config.KEGG_API_URL.format(
             operation='list', argument=db
@@ -83,7 +84,7 @@ def fetch_kegg(ID, db, output_path='.'):
     db_fmt_path = os.path.join(output_path, fmt, db)
     output_file = os.path.join(db_fmt_path, filename)
 
-    os.makedirs(db_fmt_path, exist_ok=True)
+    makedirs(db_fmt_path, exist_ok=True)
 
     url = config.KEGG_API_URL.format(operation='get', argument=ID)
 

birdy/fetcher/ncbi.py

@@ -5,6 +5,7 @@
 from Bio_Eutils import Entrez
 
 from .. import config
+from ..compat import makedirs
 from ..exceptions import ConfigurationError
 from ..utils import get_random_ids, Timer
 
@@ -52,7 +53,7 @@ def fetch_ncbi(ID, db, fmt='fasta', output_path='.'):
     db_fmt_path = os.path.join(output_path, fmt, db)
     output_file = os.path.join(db_fmt_path, filename)
 
-    os.makedirs(db_fmt_path, exist_ok=True)
+    makedirs(db_fmt_path, exist_ok=True)
 
     handle = Entrez.efetch(db=db, id=ID, rettype=fmt, retmode="text")
     response = handle.read()

birdy/fetcher/pdb.py

@@ -3,10 +3,11 @@
 import os.path
 import requests
 import sys
-import urllib.request
+from six.moves.urllib import request
 
 
 from .. import config
+from ..compat import makedirs
 from ..exceptions import NetworkError, UnsupportedFormatError
 from ..utils import get_random_ids, Timer
 
@@ -33,7 +34,7 @@ def get_pdb_ids(use_cache=True):
         logging.info("Updating PDB ids cache...")
 
         # Create cache directory if it does not exists
-        os.makedirs(config.IDS_LIST_CACHE_ROOT, exist_ok=True)
+        makedirs(config.IDS_LIST_CACHE_ROOT, exist_ok=True)
 
         # Fetch PDB ids
         response = requests.get(config.PDB_IDS_URL)
@@ -88,12 +89,12 @@ def fetch_pdb(ID, fmt='pdb', output_path='.'):
     fmt_path = os.path.join(output_path, fmt)
     output_file = os.path.join(fmt_path, filename)
 
-    os.makedirs(fmt_path, exist_ok=True)
+    makedirs(fmt_path, exist_ok=True)
 
     url = config.PDB_ID_URL.format(fmt=fmt, idx=ID[1:3], filename=filename)
 
     try:
-        urllib.request.urlretrieve(url, output_file)
+        request.urlretrieve(url, output_file)
     except:
         logging.error(
             "Cannot fetch id {id} from the PDB. Request url was: {url}".format(

birdy/wrappers/clustalw.py

@@ -13,18 +13,23 @@ def clustalw(filename):
         filename: a multi-fasta file path
 
     Returns:
-        the output alignement filename
+        the output alignment filename
     """
     logging.info("Will align {} file with clustalw".format(filename))
 
     base, ext = os.path.splitext(filename)
     log_filename = '{base}.{ext}'.format(base=base, ext='log')
 
-    cmd = '{bin} {filename}'.format(bin=config.CLUSTALW, filename=filename)
+    cmd = '{bin} {filename}'.format(
+        bin=config.CLUSTALW,
+        filename=os.path.basename(filename)
+    )
 
     try:
         with open(log_filename, "w+") as log_file:
-            subprocess.call(cmd, stdout=log_file, shell=True)
+            subprocess.call(
+                cmd, stdout=log_file, shell=True, cwd=os.path.dirname(filename)
+            )
     except:
         logging.error('Clustal alignment failed. Command was: {}'.format(cmd))
         logging.debug(sys.exc_info()[0])

requirements-dev.txt

@@ -2,3 +2,8 @@
 
 # lint
 flake8==2.4.1
+
+# tests
+pytest
+pytest-runner
+tox

requirements.txt

@@ -2,4 +2,5 @@ Bio-Eutils>=1.65
 docopt>=0.6.1
 requests>=2.7.0
 schema>=0.3.1
+six>=1.10.0
 xmltodict>=0.9.2