def run(description):
parser = argparse.ArgumentParser(
description = 'Converts input sequence file into "Boulder-IO" format, which is used by primer3',
usage = 'fastaq to_boulderio <infile> <outfile>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output files')
options = parser.parse_args()
tasks.to_boulderio(options.infile, options.outfile)
def run(description):
parser = argparse.ArgumentParser(
description=
'Converts input sequence file into "Boulder-IO" format, which is used by primer3',
usage='fastaq to_boulderio <infile> <outfile>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output files')
options = parser.parse_args()
tasks.to_boulderio(options.infile, options.outfile)
def test_to_boulderio(self):
'''Test task to_boulderio'''
tmpfile = 'tmp.boulder'
tasks.to_boulderio(
os.path.join(data_dir, 'tasks_test_to_boulderio.in.fa'), tmpfile)
self.assertTrue(
filecmp.cmp(os.path.join(data_dir,
'tasks_test_to_boulderio.out.boulder'),
tmpfile,
shallow=False))
os.unlink(tmpfile)
def test_to_boulderio(self):
'''Test task to_boulderio'''
tmpfile = 'tmp.boulder'
tasks.to_boulderio(os.path.join(data_dir, 'tasks_test_to_boulderio.in.fa'), tmpfile)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'tasks_test_to_boulderio.out.boulder'), tmpfile, shallow=False))
os.unlink(tmpfile)