def run(description):
parser = argparse.ArgumentParser(
description = description,
usage = 'fastaq replace_bases <infile> <outfile> <old> <new>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output file')
parser.add_argument('old', help='Base to be replaced')
parser.add_argument('new', help='Replace with this letter')
options = parser.parse_args()
tasks.replace_bases(options.infile, options.outfile, options.old, options.new)
def run(description):
parser = argparse.ArgumentParser(
description=description,
usage='fastaq replace_bases <infile> <outfile> <old> <new>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output file')
parser.add_argument('old', help='Base to be replaced')
parser.add_argument('new', help='Replace with this letter')
options = parser.parse_args()
tasks.replace_bases(options.infile, options.outfile, options.old,
options.new)
def test_sequences_replace_bases(self):
'''Check that fasta file gets all bases replaced OK'''
tmpfile = 'tmp.replace_bases.fa'
tasks.replace_bases(
os.path.join(data_dir, 'sequences_test_fastaq_replace_bases.fa'),
tmpfile, 'T', 'X')
self.assertTrue(
filecmp.cmp(
os.path.join(
data_dir,
'sequences_test_fastaq_replace_bases.expected.fa'),
tmpfile))
os.unlink(tmpfile)
def test_sequences_replace_bases(self):
'''Check that fasta file gets all bases replaced OK'''
tmpfile = 'tmp.replace_bases.fa'
tasks.replace_bases(os.path.join(data_dir, 'sequences_test_fastaq_replace_bases.fa'), tmpfile, 'T', 'X')
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_fastaq_replace_bases.expected.fa'), tmpfile))
os.unlink(tmpfile)
