def test_acgtn_only(self): '''Test acgtn_only''' tmpfile = 'tmp.test_acgtn_only.fa' infile = os.path.join(data_dir, 'test_acgtn_only.in.fa') expected = os.path.join(data_dir, 'test_acgtn_only.expected.fa') tasks.acgtn_only(infile, tmpfile) self.assertTrue(filecmp.cmp(expected, tmpfile, shallow=False)) os.unlink(tmpfile)
def run(description): parser = argparse.ArgumentParser( description = 'Replaces any character that is not one of acgtACGTnN with an N', usage = 'fastaq acgtn_only [options] <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.acgtn_only(options.infile, options.outfile)
def run(description): parser = argparse.ArgumentParser( description= 'Replaces any character that is not one of acgtACGTnN with an N', usage='fastaq acgtn_only [options] <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.acgtn_only(options.infile, options.outfile)