From 6f99120e13663a472837c2c884b3e09a6f106f5a Mon Sep 17 00:00:00 2001
From: Andrew Waterhouse <andrew.waterhouse@unibas.ch>
Date: Thu, 14 Jun 2012 16:29:32 +0200
Subject: [PATCH] convert ? to X before running clustalw
---
modules/bindings/pymod/clustalw.py | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/modules/bindings/pymod/clustalw.py b/modules/bindings/pymod/clustalw.py
index 2c2fd6eba..2795f66dd 100644
--- a/modules/bindings/pymod/clustalw.py
+++ b/modules/bindings/pymod/clustalw.py
@@ -27,6 +27,13 @@ def ClustalW(seq1, seq2=None, clustalw=None, keep_files=False, nopgap=False,
else:
LogError("WARNING: Specify either two SequenceHandles or one SequenceList")
return
+
+ new_list = seq.CreateSequenceList()
+ for s in seq_list:
+ ss = seq.CreateSequence( s.GetName(), s.GetString().replace('?','X') )
+ new_list.AddSequence(ss)
+
+ seq_list = new_list
temp_dir=utils.TempDirWithFiles((seq_list,))
out=os.path.join(temp_dir.dirname, 'out.fasta')
--
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