def run(description):
parser = argparse.ArgumentParser(
description = 'Trims any Ns off each sequence in input file. Does nothing to gaps in the middle, just trims the ends',
usage = 'fastaq trim_Ns_at_end <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.trim_Ns_at_end(options.infile, options.outfile)
def test_trim_Ns_at_end(self):
'''Test Ns at ends of sequences trimmed OK'''
tmp = 'tmp.trim.fa'
tasks.trim_Ns_at_end(
os.path.join(data_dir, 'sequences_test_trim_Ns_at_end.fa'), tmp)
self.assertTrue(
filecmp.cmp(
os.path.join(data_dir,
'sequences_test_trim_Ns_at_end.fa.trimmed'), tmp))
os.unlink(tmp)
def test_trim_Ns_at_end(self):
'''Test Ns at ends of sequences trimmed OK'''
tmp = 'tmp.trim.fa'
tasks.trim_Ns_at_end(os.path.join(data_dir, 'sequences_test_trim_Ns_at_end.fa'), tmp)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_trim_Ns_at_end.fa.trimmed'), tmp))
os.unlink(tmp)
