def process_nxmate_reads(dataset_data, dst, log):
try:
import lucigen_nxmate
new_dataset_data = list()
for reads_library in dataset_data:
new_reads_library = dict(reads_library)
if new_reads_library['type'] == 'nxmate':
raw_left_reads = new_reads_library['left reads']
raw_right_reads = new_reads_library['right reads']
new_reads_library['left reads'] = []
new_reads_library['right reads'] = []
new_reads_library['single reads'] = []
for id, left_reads_fpath in enumerate(raw_left_reads):
right_reads_fpath = raw_right_reads[id]
processed_left_reads_fpath, processed_right_reads_fpath, single_reads_fpath = \
lucigen_nxmate.process_reads(left_reads_fpath, right_reads_fpath, dst, log)
new_reads_library['left reads'].append(
processed_left_reads_fpath)
new_reads_library['right reads'].append(
processed_right_reads_fpath)
new_reads_library['single reads'].append(
single_reads_fpath)
new_reads_library['type'] = 'mate-pairs'
new_reads_library['orientation'] = 'fr'
new_dataset_data.append(new_reads_library)
return new_dataset_data
except ImportError:
error(
"Can't process Lucigen NxMate reads! lucigen_nxmate.py is missing!",
log)
def process_nxmate_reads(dataset_data, dst, log):
try:
import lucigen_nxmate
new_dataset_data = list()
for reads_library in dataset_data:
new_reads_library = dict(reads_library)
if new_reads_library['type'] == 'nxmate':
raw_left_reads = new_reads_library['left reads']
raw_right_reads = new_reads_library['right reads']
new_reads_library['left reads'] = []
new_reads_library['right reads'] = []
new_reads_library['single reads'] = []
for id, left_reads_fpath in enumerate(raw_left_reads):
right_reads_fpath = raw_right_reads[id]
processed_left_reads_fpath, processed_right_reads_fpath, single_reads_fpath = \
lucigen_nxmate.process_reads(left_reads_fpath, right_reads_fpath, dst, log)
new_reads_library['left reads'].append(processed_left_reads_fpath)
new_reads_library['right reads'].append(processed_right_reads_fpath)
new_reads_library['single reads'].append(single_reads_fpath)
new_reads_library['type'] = 'mate-pairs'
new_reads_library['orientation'] = 'fr'
new_dataset_data.append(new_reads_library)
return new_dataset_data
except ImportError:
error("Can't process Lucigen NxMate reads! lucigen_nxmate.py is missing!", log)
def main():
args = parse_args()
# create logger
log = logging.getLogger("Preprocess Lucigen NxMate reads")
log.setLevel(logging.DEBUG)
console = logging.StreamHandler(sys.stdout)
console.setFormatter(logging.Formatter("%(message)s"))
console.setLevel(logging.DEBUG)
log.addHandler(console)
try:
with open(args.args_filename) as f:
lines = f.readlines()
for infile1, infile2 in zip(lines[0::2], lines[1::2]):
lucigen_nxmate.process_reads(infile1, infile2, args.dst, log,
args.threads)
except ImportError:
support.error(
"can't process Lucigen NxMate reads! lucigen_nxmate.py is missing!",
log)