Ejemplo n.º 1
0
    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')
Ejemplo n.º 2
0
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)
Ejemplo n.º 3
0
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)