/tools/genetrack/genetrack_indexer.py
https://bitbucket.org/cistrome/cistrome-harvard/ · Python · 42 lines · 23 code · 10 blank · 9 comment · 6 complexity · 69ba8cb3ca1b0b83d968098a825cafcf MD5 · raw file
- #!/usr/bin/env python
- """
- Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy.
- usage: %prog input output shift
- """
- import sys, shutil, os
- from galaxy import eggs
- import pkg_resources
- pkg_resources.require( "GeneTrack" )
- from genetrack.scripts import tabs2genetrack
- from genetrack import logger
- if __name__ == "__main__":
- import os
- os.environ[ 'LC_ALL' ] = 'C'
- #os.system( 'export' )
-
- parser = tabs2genetrack.option_parser()
- options, args = parser.parse_args()
- # uppercase the format
- options.format = options.format.upper()
- if options.format not in ('BED', 'GFF'):
- sys.stdout = sys.stderr
- parser.print_help()
- sys.exit(-1)
- logger.disable(options.verbosity)
- # missing file names
- if not (options.inpname and options.outname and options.format):
- parser.print_help()
- sys.exit(-1)
- else:
- tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\
- format=options.format, shift=options.shift, index=options.index, options=options)