From 46805eb07d386e59ab89955c2e9c573ef34f6adb Mon Sep 17 00:00:00 2001
From: Stefan Bienert <stefan.bienert@unibas.ch>
Date: Tue, 18 Aug 2015 16:35:12 +0200
Subject: [PATCH] Simplifying handling fasta
---
core/pymod/core/pm3argparse.py | 29 +++++++++++++++++++----------
core/tests/test_pm3argparse.py | 2 +-
2 files changed, 20 insertions(+), 11 deletions(-)
diff --git a/core/pymod/core/pm3argparse.py b/core/pymod/core/pm3argparse.py
index 8233e289..a606c81f 100644
--- a/core/pymod/core/pm3argparse.py
+++ b/core/pymod/core/pm3argparse.py
@@ -213,6 +213,24 @@ class PM3OptionsNamespace(object):
if 'ALIGNMENT' in activated:
self._PostProcessAlignment()
+ def _FetchAlnFromFastaOpt(self, argstr):
+ """
+ Dissasemble an argument to '--fasta' into an alignment and return.
+ """
+ # get which element of the argument list is the target identifier and
+ # which one is the filename
+ if argstr[0].startswith('trg:'):
+ trgname = argstr[0][4:]
+ seqfile = argstr[1]
+ elif argstr[1].startswith('trg:'):
+ trgname = argstr[1][4:]
+ seqfile = argstr[0]
+ else:
+ helper.MsgErrorAndExit("'--fasta %s' requires " % ' '.join(argstr)+
+ "one argument prefixed with 'trg:' marking "+
+ "the target sequence name", 11)
+ return trgname, seqfile
+
def _PostProcessAlignment(self):
#pylint: disable=no-member
#pylint: disable=attribute-defined-outside-init
@@ -223,16 +241,7 @@ class PM3OptionsNamespace(object):
self.alignments = seq.AlignmentList()
if self.fasta:
for src in self.fasta:
- if src[0].startswith('trg:'):
- trgname = src[0][4:]
- seqfile = src[1]
- elif src[1].startswith('trg:'):
- trgname = src[1][4:]
- seqfile = src[0]
- else:
- helper.MsgErrorAndExit("'--fasta' requires one argument "+
- "prefixed with 'trg:' marking the "+
- "target sequence name", 11)
+ trgname, seqfile = self._FetchAlnFromFastaOpt(src)
if not len(trgname):
helper.MsgErrorAndExit("'--fasta' requires argument "+
"'trg:' defining the "+
diff --git a/core/tests/test_pm3argparse.py b/core/tests/test_pm3argparse.py
index cc2f4aed..10ad2777 100644
--- a/core/tests/test_pm3argparse.py
+++ b/core/tests/test_pm3argparse.py
@@ -87,7 +87,7 @@ class PM3ArgParseTests(unittest.TestCase):
parser.Parse(['--fasta', 'foo', 'bar'])
self.assertEqual(ecd.exception.code, 11)
self.assertEqual(self.log.messages['ERROR'][0],
- "'--fasta' requires one "+
+ "'--fasta foo bar' requires one "+
"argument prefixed with 'trg:' marking the target "+
"sequence name")
--
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