def test_tabs2genetrack(self): "Testing bed2genetrack transformation" from genetrack.scripts import tabs2genetrack inpfile = conf.testdata('short-data.bed', verify=True) outfile = conf.tempdata('short-data.genetrack') tabs2genetrack.transform(inpfile, outfile, format='BED')
from galaxy import eggs import pkg_resources pkg_resources.require( "GeneTrack" ) from genetrack.scripts import tabs2genetrack from genetrack import logger if __name__ == "__main__": 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)
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)