def run(description):
parser = argparse.ArgumentParser(
description = 'Splits a multi sequence file into separate files. Splits sequences into chunks of a fixed size. Aims for chunk_size chunks in each file, but allows a little extra, so chunk can be up to (chunk_size + tolerance), to prevent tiny chunks made from the ends of sequences',
usage = 'fastaq chunker [options] <infile> <out> <chunk size> <tolerance>')
parser.add_argument('infile', help='Name of input file to be split')
parser.add_argument('out', help='Prefix of output file. If --onefile used, then name of single output file')
parser.add_argument('chunk_size', type=int, help='Size of each chunk')
parser.add_argument('tolerance', type=int, help='Tolerance allowed in chunk size')
parser.add_argument('--onefile', action='store_true', help='Output all the sequences in one file')
parser.add_argument('--skip_all_Ns', action='store_true', help='Do not output any sequence that consists of all Ns')
options = parser.parse_args()
if options.onefile:
tasks.split_by_fixed_size_onefile(
options.infile,
options.out,
options.chunk_size,
options.tolerance,
skip_if_all_Ns=options.skip_all_Ns
)
else:
tasks.split_by_fixed_size(
options.infile,
options.out,
options.chunk_size,
options.tolerance,
skip_if_all_Ns=options.skip_all_Ns
)
def test_split_by_fixed_size_exclude_Ns(self):
infile = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa')
outprefix = 'tmp.sequences_test_split'
tasks.split_by_fixed_size(infile, outprefix, 4, 1, skip_if_all_Ns=True)
for i in range(1,5,1):
correct = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.' + str(i))
test = outprefix + '.' + str(i)
self.assertTrue(filecmp.cmp(test, correct))
os.unlink(test)
test_coords = outprefix + '.coords'
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.coords'), test_coords))
os.unlink(test_coords)
def test_split_by_fixed_size_exclude_Ns(self):
infile = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa')
outprefix = 'tmp.sequences_test_split'
tasks.split_by_fixed_size(infile, outprefix, 4, 1, skip_if_all_Ns=True)
for i in range(1,5,1):
correct = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.' + str(i))
test = outprefix + '.' + str(i)
self.assertTrue(filecmp.cmp(test, correct))
os.unlink(test)
test_coords = outprefix + '.coords'
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.skip_if_all_Ns.coords'), test_coords))
os.unlink(test_coords)
def test_split_by_fixed_size(self):
'''Test fasta/q file split by fixed size'''
infile = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa')
outprefix = 'tmp.sequences_test_split'
tasks.split_by_fixed_size(infile, outprefix, 4, 1)
for i in range(1,7,1):
correct = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.' + str(i))
test = outprefix + '.' + str(i)
self.assertTrue(filecmp.cmp(test, correct))
os.unlink(test)
test_coords = outprefix + '.coords'
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.coords'), test_coords))
os.unlink(test_coords)
def test_split_by_fixed_size(self):
'''Test fasta/q file split by fixed size'''
infile = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa')
outprefix = 'tmp.sequences_test_split'
tasks.split_by_fixed_size(infile, outprefix, 4, 1)
for i in range(1,7,1):
correct = os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.' + str(i))
test = outprefix + '.' + str(i)
self.assertTrue(filecmp.cmp(test, correct))
os.unlink(test)
test_coords = outprefix + '.coords'
self.assertTrue(filecmp.cmp(os.path.join(data_dir, 'sequences_test_split_fixed_size.fa.split.coords'), test_coords))
os.unlink(test_coords)
def run(description):
parser = argparse.ArgumentParser(
description=
'Splits a multi sequence file into separate files. Splits sequences into chunks of a fixed size. Aims for chunk_size chunks in each file, but allows a little extra, so chunk can be up to (chunk_size + tolerance), to prevent tiny chunks made from the ends of sequences',
usage='fastaq chunker [options] <infile> <out> <chunk size> <tolerance>'
)
parser.add_argument('infile', help='Name of input file to be split')
parser.add_argument(
'out',
help=
'Prefix of output file. If --onefile used, then name of single output file'
)
parser.add_argument('chunk_size', type=int, help='Size of each chunk')
parser.add_argument('tolerance',
type=int,
help='Tolerance allowed in chunk size')
parser.add_argument('--onefile',
action='store_true',
help='Output all the sequences in one file')
parser.add_argument(
'--skip_all_Ns',
action='store_true',
help='Do not output any sequence that consists of all Ns')
options = parser.parse_args()
if options.onefile:
tasks.split_by_fixed_size_onefile(options.infile,
options.out,
options.chunk_size,
options.tolerance,
skip_if_all_Ns=options.skip_all_Ns)
else:
tasks.split_by_fixed_size(options.infile,
options.out,
options.chunk_size,
options.tolerance,
skip_if_all_Ns=options.skip_all_Ns)
