From 67c858c8b55852bb68134ea5b9ed4a0cdfb7cd41 Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 18 Aug 2015 17:39:29 +0200
Subject: [PATCH] Simplification
---
core/pymod/core/pm3argparse.py | 59 ++++++++++++++++++----------------
core/tests/test_pm3argparse.py | 4 +--
2 files changed, 33 insertions(+), 30 deletions(-)
diff --git a/core/pymod/core/pm3argparse.py b/core/pymod/core/pm3argparse.py
index 69601078..3765ecf1 100644
--- a/core/pymod/core/pm3argparse.py
+++ b/core/pymod/core/pm3argparse.py
@@ -235,9 +235,38 @@ class PM3OptionsNamespace(object):
"argument 'trg:' defining the "+
"target sequence name, empty one "+
"found: '%s'" % ' '.join(argstr), 14)
+ # checking that alignment file exists
helper.FileExists("Alignment", 12, seqfile)
+ # checking if alignment file has 'gz' extension
is_gz = helper.FileGzip("Alignment", 13, seqfile)
- return trgname, seqfile, is_gz
+ # loading the alignment, switch for gzip
+ readfile = seqfile
+ if is_gz:
+ zip_fh = gzip.open(seqfile)
+ unzip_str = zip_fh.read()
+ zip_fh.close()
+ unzip_file = tempfile.NamedTemporaryFile(mode='w',
+ suffix='.fas')
+ unzip_file.write(unzip_str)
+ unzip_file.flush()
+ readfile = unzip_file.name
+ try:
+ aln = io.LoadAlignment(readfile, format="fasta")
+ except Exception, exc: #pylint: disable=broad-except
+ if exc.message == 'Bad FASTA file: File is empty':
+ helper.MsgErrorAndExit("'--fasta %s' " % ' '.join(argstr)+
+ "refers to an empty file or its in the "+
+ "wrong format.", 15)
+ elif exc.message == 'sequences have different lengths':
+ helper.MsgErrorAndExit("'--fasta %s': " % ' '.join(argstr)+
+ "sequences in the alignment "+
+ "have different length.", 18)
+ else:
+ raise
+ finally:
+ if is_gz:
+ unzip_file.close()
+ return trgname, seqfile, is_gz, aln
def _PostProcessAlignment(self):
#pylint: disable=no-member
@@ -249,33 +278,7 @@ class PM3OptionsNamespace(object):
self.alignments = seq.AlignmentList()
if self.fasta:
for src in self.fasta:
- trgname, seqfile, is_gz = self._FetchAlnFromFastaOpt(src)
- readfile = seqfile
- if is_gz:
- zip_fh = gzip.open(seqfile)
- unzip_str = zip_fh.read()
- zip_fh.close()
- unzip_file = tempfile.NamedTemporaryFile(mode='w',
- suffix='.fas')
- unzip_file.write(unzip_str)
- unzip_file.flush()
- readfile = unzip_file.name
- try:
- aln = io.LoadAlignment(readfile, format="fasta")
- except Exception, exc: #pylint: disable=broad-except
- if exc.message == 'Bad FASTA file: File is empty':
- helper.MsgErrorAndExit("'--fasta' refers to an empty "+\
- "file or its in the wrong "+
- "format: %s" % seqfile, 15)
- elif exc.message == 'sequences have different lengths':
- helper.MsgErrorAndExit("'--fasta %s': " % ' '.join(src)+
- "sequences in the alignment "+
- "have different length.", 18)
- else:
- raise
- finally:
- if is_gz:
- unzip_file.close()
+ trgname, seqfile, is_gz, aln = self._FetchAlnFromFastaOpt(src)
# check alignment
nos = aln.GetCount()
if nos > 2:
diff --git a/core/tests/test_pm3argparse.py b/core/tests/test_pm3argparse.py
index 948d20f1..8bd20a84 100644
--- a/core/tests/test_pm3argparse.py
+++ b/core/tests/test_pm3argparse.py
@@ -163,8 +163,8 @@ class PM3ArgParseTests(unittest.TestCase):
parser.Parse(['--fasta', 'trg:foo', 'data/fasta/alignment.fas'])
self.assertEqual(ecd.exception.code, 15)
self.assertEqual(self.log.messages['ERROR'][0],
- "'--fasta' refers to an empty file or its in the "+
- "wrong format: data/fasta/alignment.fas")
+ "'--fasta trg:foo data/fasta/alignment.fas' refers "+
+ "to an empty file or its in the wrong format.")
def testAddAlignmentToMany(self):
parser = pm3argparse.PM3ArgumentParser(__doc__, action=False)
--
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