def run(description):
parser = argparse.ArgumentParser(
description = 'Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input',
usage = 'fastaq scaffolds_to_contigs [options] <infile> <outfile>')
parser.add_argument('--number_contigs', action='store_true', help='Use this to enumerate contig names 1,2,3,... within each scaffold')
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output contigs file')
options = parser.parse_args()
tasks.scaffolds_to_contigs(options.infile, options.outfile, number_contigs=options.number_contigs)
def test_scaffolds_to_contigs(self):
'''Test scaffolds_to_contigs'''
tmp = 'tmp.contigs.fa'
tasks.scaffolds_to_contigs(
os.path.join(data_dir, 'utils_test_scaffolds.fa'), tmp)
self.assertTrue(
filecmp.cmp(
os.path.join(data_dir,
'utils_test_scaffolds.fa.to_contigs.fa'), tmp))
os.unlink(tmp)
def test_scaffolds_to_contigs_number_contigs(self):
'''Test scaffolds_to_contigs with contig numbering'''
tmp = 'tmp.contigs.fa'
tasks.scaffolds_to_contigs(os.path.join(data_dir,
'utils_test_scaffolds.fa'),
tmp,
number_contigs=True)
self.assertTrue(
filecmp.cmp(
os.path.join(
data_dir,
'utils_test_scaffolds.fa.to_contigs.number_contigs.fa'),
tmp))
os.unlink(tmp)
def run(description):
parser = argparse.ArgumentParser(
description=
'Creates a file of contigs from a file of scaffolds - i.e. breaks at every gap in the input',
usage='fastaq scaffolds_to_contigs [options] <infile> <outfile>')
parser.add_argument(
'--number_contigs',
action='store_true',
help='Use this to enumerate contig names 1,2,3,... within each scaffold'
)
parser.add_argument('infile', help='Name of input file')
parser.add_argument('outfile', help='Name of output contigs file')
options = parser.parse_args()
tasks.scaffolds_to_contigs(options.infile,
options.outfile,
number_contigs=options.number_contigs)
def test_scaffolds_to_contigs_number_contigs(self):
'''Test scaffolds_to_contigs with contig numbering'''
tmp = 'tmp.contigs.fa'
tasks.scaffolds_to_contigs(os.path.join(data_dir, 'utils_test_scaffolds.fa'), tmp, number_contigs=True)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'utils_test_scaffolds.fa.to_contigs.number_contigs.fa'), tmp))
os.unlink(tmp)
def test_scaffolds_to_contigs(self):
'''Test scaffolds_to_contigs'''
tmp = 'tmp.contigs.fa'
tasks.scaffolds_to_contigs(os.path.join(data_dir, 'utils_test_scaffolds.fa'), tmp)
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'utils_test_scaffolds.fa.to_contigs.fa'), tmp))
os.unlink(tmp)