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)