def run(description):
parser = argparse.ArgumentParser(
description='Gets IDs from each sequence in input file',
usage='fastaq get_ids <infile> <outfile>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output file')
options = parser.parse_args()
tasks.get_ids(options.infile, options.outfile)
def test_get_ids(self):
'''Check that IDs extracted correctly from fasta/q file'''
tmpfile = 'tmp.ids'
tasks.get_ids(os.path.join(data_dir, 'sequences_test.fa'), tmpfile)
self.assertTrue(
filecmp.cmp(os.path.join(data_dir, 'sequences_test.fa.ids'),
tmpfile))
os.unlink(tmpfile)
def run(description):
parser = argparse.ArgumentParser(
description = 'Gets IDs from each sequence in input file',
usage = 'fastaq get_ids <infile> <outfile>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output file')
options = parser.parse_args()
tasks.get_ids(options.infile, options.outfile)
def test_get_ids(self):
'''Check that IDs extracted correctly from fasta/q file'''
tmpfile = 'tmp.ids'
tasks.get_ids(os.path.join(data_dir, 'sequences_test.fa'), tmpfile)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test.fa.ids'), tmpfile))
os.unlink(tmpfile)
