Mercurial > repos > iuc > jbrowse

diff blastxml_to_gapped_gff3.py @ 12:db5fe5a3176a draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse commit 2bfbb5ae6b801e43355fdc3f964a5111fe3fe3a1
author iuc
date Mon, 06 Feb 2017 12:52:09 -0500
parents ad4b9d7eae6a
children 18be2d72fdee
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line diff
--- a/blastxml_to_gapped_gff3.py	Wed Dec 14 09:19:48 2016 -0500
+++ b/blastxml_to_gapped_gff3.py	Mon Feb 06 12:52:09 2017 -0500
@@ -253,7 +253,7 @@
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='')
-    parser.add_argument('blastxml', type=file, help='Blast XML Output')
+    parser.add_argument('blastxml', type=open, help='Blast XML Output')
     parser.add_argument('--min_gap', type=int, help='Maximum gap size before generating a new match_part', default=3)
     parser.add_argument('--trim', action='store_true', help='Trim blast hits to be only as long as the parent feature')
     parser.add_argument('--trim_end', action='store_true', help='Cut blast results off at end of gene')