Mercurial > repos > iuc > jbrowse

comparison 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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11:4cbceec1d6b4 12:db5fe5a3176a
251 return "" 251 return ""
252 252
253 253
254 if __name__ == '__main__': 254 if __name__ == '__main__':
255 parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='') 255 parser = argparse.ArgumentParser(description='Convert Blast XML to gapped GFF3', epilog='')
256 parser.add_argument('blastxml', type=file, help='Blast XML Output') 256 parser.add_argument('blastxml', type=open, help='Blast XML Output')
257 parser.add_argument('--min_gap', type=int, help='Maximum gap size before generating a new match_part', default=3) 257 parser.add_argument('--min_gap', type=int, help='Maximum gap size before generating a new match_part', default=3)
258 parser.add_argument('--trim', action='store_true', help='Trim blast hits to be only as long as the parent feature') 258 parser.add_argument('--trim', action='store_true', help='Trim blast hits to be only as long as the parent feature')
259 parser.add_argument('--trim_end', action='store_true', help='Cut blast results off at end of gene') 259 parser.add_argument('--trim_end', action='store_true', help='Cut blast results off at end of gene')
260 args = parser.parse_args() 260 args = parser.parse_args()
261 261