/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

  1. #!/usr/bin/env python
  2. """
  3. Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy.
  4. usage: %prog input output shift
  5. """
  6. import sys, shutil, os
  7. from galaxy import eggs
  8. import pkg_resources
  9. pkg_resources.require( "GeneTrack" )
  10. from genetrack.scripts import tabs2genetrack
  11. from genetrack import logger
  12. if __name__ == "__main__":
  13. import os
  14. os.environ[ 'LC_ALL' ] = 'C'
  15. #os.system( 'export' )
  16. parser = tabs2genetrack.option_parser()
  17. options, args = parser.parse_args()
  18. # uppercase the format
  19. options.format = options.format.upper()
  20. if options.format not in ('BED', 'GFF'):
  21. sys.stdout = sys.stderr
  22. parser.print_help()
  23. sys.exit(-1)
  24. logger.disable(options.verbosity)
  25. # missing file names
  26. if not (options.inpname and options.outname and options.format):
  27. parser.print_help()
  28. sys.exit(-1)
  29. else:
  30. tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\
  31. format=options.format, shift=options.shift, index=options.index, options=options)