Mercurial > repos > boris > getalleleseq

changeset 2:ac2d160ccc1b draft

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Replaced getalleleseq.py to solve a Galaxy output handling issue
author boris
date Thu, 30 May 2013 15:30:26 -0400
parents fac328fae4cb
children bb8234491756
files getalleleseq/getalleleseq.py
diffstat 1 files changed, 2 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/getalleleseq/getalleleseq.py	Wed May 29 09:29:35 2013 -0400
+++ b/getalleleseq/getalleleseq.py	Thu May 30 15:30:26 2013 -0400
@@ -106,7 +106,8 @@
 
     for sample in samples:
         if args.minor_prefix: # to fit Galaxy requirements
-            minor_name = "%s_%s_%s" % ('primary',args.minor_prefix,sample+'-minor_visible_fasta')
+            name = sample.replace('_','')
+            minor_name = "%s_%s_%s" % ('primary',args.minor_prefix,name+'-minor_visible_fasta')
         else: # for non-Galaxy 
             minor_name = sample+'-minor.fa'
         minor_out = open(os.path.join(args.minor_dir, minor_name), 'w+')