# HG changeset patch
# User boris
# Date 1369942226 14400
# Node ID ac2d160ccc1b15ea2ae3de463991bdf9c8dc51b5
# Parent  fac328fae4cb25fd9021a2cbab7060c16a22a8d6
Replaced getalleleseq.py to solve a Galaxy output handling issue

diff -r fac328fae4cb -r ac2d160ccc1b getalleleseq/getalleleseq.py
--- 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+')