From 7b44a3d62704b11292c8c209468571823fdff20a Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 18 Aug 2015 17:14:03 +0200
Subject: [PATCH] Simplifications
---
core/pymod/core/pm3argparse.py | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/core/pymod/core/pm3argparse.py b/core/pymod/core/pm3argparse.py
index dd4c981f..69601078 100644
--- a/core/pymod/core/pm3argparse.py
+++ b/core/pymod/core/pm3argparse.py
@@ -235,7 +235,9 @@ class PM3OptionsNamespace(object):
"argument 'trg:' defining the "+
"target sequence name, empty one "+
"found: '%s'" % ' '.join(argstr), 14)
- return trgname, seqfile
+ helper.FileExists("Alignment", 12, seqfile)
+ is_gz = helper.FileGzip("Alignment", 13, seqfile)
+ return trgname, seqfile, is_gz
def _PostProcessAlignment(self):
#pylint: disable=no-member
@@ -247,9 +249,7 @@ class PM3OptionsNamespace(object):
self.alignments = seq.AlignmentList()
if self.fasta:
for src in self.fasta:
- trgname, seqfile = self._FetchAlnFromFastaOpt(src)
- helper.FileExists("Alignment", 12, seqfile)
- is_gz = helper.FileGzip("Alignment", 13, seqfile)
+ trgname, seqfile, is_gz = self._FetchAlnFromFastaOpt(src)
readfile = seqfile
if is_gz:
zip_fh = gzip.open(seqfile)
--
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