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)