def test_trim(self):
'''trim should correctly trim each seq in a file'''
tmp = 'tmp.trim.fq'
tasks.trim(os.path.join(data_dir, 'sequences_test_untrimmed.fq'), tmp,
2, 1)
self.assertTrue(
filecmp.cmp(os.path.join(data_dir, 'sequences_test_trimmed.fq'),
tmp))
os.unlink(tmp)
def run(description):
parser = argparse.ArgumentParser(
description = description,
usage = 'fastaq trim_ends <infile> <bases off start> <bases off end> <outfile>')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('start_trim', type=int, help='Number of bases to trim off start')
parser.add_argument('end_trim', type=int, help='Number of bases to trim off end')
parser.add_argument('outfile', help='Name of output file')
options = parser.parse_args()
tasks.trim(options.infile, options.outfile, options.start_trim, options.end_trim)
def run(description):
parser = argparse.ArgumentParser(
description=description,
usage=
'fastaq trim_ends <infile> <bases off start> <bases off end> <outfile>'
)
parser.add_argument('infile', help='Name of input file')
parser.add_argument('start_trim',
type=int,
help='Number of bases to trim off start')
parser.add_argument('end_trim',
type=int,
help='Number of bases to trim off end')
parser.add_argument('outfile', help='Name of output file')
options = parser.parse_args()
tasks.trim(options.infile, options.outfile, options.start_trim,
options.end_trim)
def test_trim(self):
'''trim should correctly trim each seq in a file'''
tmp = 'tmp.trim.fq'
tasks.trim(os.path.join(data_dir, 'sequences_test_untrimmed.fq'), tmp, 2, 1)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_trimmed.fq'), tmp))
os.unlink(tmp)
