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)
