def run(description): parser = argparse.ArgumentParser( description = 'Writes a GFF file of open reading frames from a sequence file', usage = 'fastaq to_orfs_gff [options] <infile> <outfile>') parser.add_argument('--min_length', type=int, help='Minimum length of ORF, in nucleotides [%(default)s]', default=300, metavar='INT') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output GFF file') options = parser.parse_args() tasks.fastaq_to_orfs_gff(options.infile, options.outfile, min_length=options.min_length)
def test_fastaq_to_orfs_gff(self): '''Test fastaq_to_orfs_gff''' outfile = 'tmp.orfs.gff' tasks.fastaq_to_orfs_gff(os.path.join(data_dir, 'sequences_test_orfs.fa'), outfile, min_length=120) self.assertTrue( filecmp.cmp(os.path.join(data_dir, 'sequences_test_orfs.gff'), outfile, shallow=False)) os.unlink(outfile)
def run(description): parser = argparse.ArgumentParser( description= 'Writes a GFF file of open reading frames from a sequence file', usage='fastaq to_orfs_gff [options] <infile> <outfile>') parser.add_argument( '--min_length', type=int, help='Minimum length of ORF, in nucleotides [%(default)s]', default=300, metavar='INT') parser.add_argument('infile', help='Name of input file') parser.add_argument('outfile', help='Name of output GFF file') options = parser.parse_args() tasks.fastaq_to_orfs_gff(options.infile, options.outfile, min_length=options.min_length)
def test_fastaq_to_orfs_gff(self): '''Test fastaq_to_orfs_gff''' outfile = 'tmp.orfs.gff' tasks.fastaq_to_orfs_gff(os.path.join(data_dir, 'sequences_test_orfs.fa'), outfile, min_length=120) self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_orfs.gff'), outfile, shallow=False)) os.unlink(outfile)