From df439707f0c757bbb58526634c47b38a36aba580 Mon Sep 17 00:00:00 2001
From: juergen <juergen@5a81b35b-ba03-0410-adc8-b2c5c5119f08>
Date: Mon, 3 May 2010 16:20:27 +0000
Subject: [PATCH] optimising handling properties of sequences in clustalw
wrapper
git-svn-id: https://dng.biozentrum.unibas.ch/svn/openstructure/trunk@2171 5a81b35b-ba03-0410-adc8-b2c5c5119f08
---
modules/bindings/pymod/clustalw.py | 19 ++++++++-----------
1 file changed, 8 insertions(+), 11 deletions(-)
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index 38678cc78..fdf024ebc 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -16,17 +16,14 @@ def ClustalW(seq1, seq2, clustalw=None):
out)
ps=subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
ps.stdout.readlines()
- taln=io.LoadAlignment(out)
- aln=seq.CreateAlignment()
- if (seq1.HasAttachedView() and seq2.HasAttachedView()):
- seq00=taln.GetSequence(0).Copy()
- seq00.AttachView(seq1.GetAttachedView().Copy())
- seq01=taln.GetSequence(1).Copy()
- seq01.AttachView(seq2.GetAttachedView().Copy())
- aln.AddSequence(seq00)
- aln.AddSequence(seq01)
- else:
- aln=taln.Copy()
+ aln=io.LoadAlignment(out)
+ aln.SetSequenceOffset(0,seq1.GetSequenceOffset())
+ aln.SetSequenceOffset(1,seq2.GetSequenceOffset())
+ if seq1.HasAttachedView():
+ aln.AttachView(0,seq1.GetAttachedView().Copy())
+ if seq2.HasAttachedView():
+ aln.AttachView(1,seq2.GetAttachedView().Copy())
+
#~ temp_dir.Cleanup()
--
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