From 2b49db760fa4000e65fbe8fb018459b36ddf3082 Mon Sep 17 00:00:00 2001
From: Tobias Schmidt <tobias.schmidt@unibas.ch>
Date: Wed, 3 Nov 2010 15:51:07 +0100
Subject: [PATCH] fixed clustalw binding, additional unittest
---
modules/bindings/pymod/clustalw.py | 4 ++--
modules/bindings/tests/test_clustalw.py | 9 +++++++++
2 files changed, 11 insertions(+), 2 deletions(-)
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index e737cea57..6f0434da5 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -13,8 +13,8 @@ def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, nopgap=False):
seq_list.AddSequence(seq1)
seq_list.AddSequence(seq2)
elif isinstance(seq1, str) and isinstance(seq2, str):
- seqh1=CreateSequence("seq1", seq1)
- seqh2=CreateSequence("seq2", seq2)
+ seqh1=seq.CreateSequence("seq1", seq1)
+ seqh2=seq.CreateSequence("seq2", seq2)
seq_list=seq.CreateSequenceList()
seq_list.AddSequence(seqh1)
seq_list.AddSequence(seqh2)
diff --git a/modules/bindings/tests/test_clustalw.py b/modules/bindings/tests/test_clustalw.py
index cf8b2753e..010b636eb 100644
--- a/modules/bindings/tests/test_clustalw.py
+++ b/modules/bindings/tests/test_clustalw.py
@@ -15,6 +15,8 @@ class TestClustalWBindings(unittest.TestCase):
self.pw_alignment = io.LoadAlignment("testfiles/pairwise_aln.fasta")
self.nopgap_pw_alignment = io.LoadAlignment("testfiles/nopgap_pairwise_aln.fasta")
self.mult_alignment = io.LoadAlignment("testfiles/multiple_aln.fasta")
+ self.strseq1 = self.targetseq.GetGaplessString()
+ self.strseq2 = self.templseq.GetGaplessString()
def testPairwiseClustalW(self):
aln=clustalw.ClustalW(self.targetseq, self.templseq)
@@ -36,6 +38,13 @@ class TestClustalWBindings(unittest.TestCase):
assert self.mult_alignment.ToString(80) == aln.ToString(80), \
"Multiple alignment differs from precomputed one"
+ def testStringClustalW(self):
+ aln=clustalw.ClustalW(self.strseq1, self.strseq2)
+ aln.SetSequenceName(0,self.targetseq.GetName())
+ aln.SetSequenceName(1,self.templseq.GetName())
+ assert self.pw_alignment.ToString(80) == aln.ToString(80), \
+ "Pairwise alignment using two strings differs from precomputed one \n%s \n%s" \
+ %(self.pw_alignment.ToString(80),aln.ToString(80))
if __name__ == "__main__":
# test if clustalw package is available on system, otherwise ignore tests
--
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