def process_fastq(
input_file, output_prefix, logger_name="fastq_processing", log_itvl=1000000
):
"""
Processes the provided fastq file and splits into 1 or more separate
readgroup level fastq files.
:param input_file: input fastq file path
:param output_prefix: output prefix
:param loggger_name: name of the logger created
:param log_itvl: print log every N records
:return: a tuple containing dictionary of report and total counts
"""
logger = get_logger(logger_name)
ibase = os.path.basename(input_file)
logger.info("Processing fastq: {0}".format(ibase))
fq_cls = infer_fastq_type(input_file)
logger.info("Inferred fastq class {0} in fastq {1}".format(fq_cls[0], ibase))
reader = FastqReader(input_file, record_cls=fq_cls[1])
count = 0
writers = {}
try:
for record in reader:
count += 1
if count % log_itvl == 0:
logger.info("Processed {0} records from {1}".format(count, ibase))
key = record.read_key
if key not in writers:
logger.info("Found read key {0} in fastq {1}".format(key, ibase))
writer = FastqWriterWithReport.from_record_and_prefix(
record, output_prefix
)
logger.info(
"Output file for read key {0} in fastq {1} is {2}".format(
key, ibase, writer.fname
)
)
writers[key] = writer
writers[key] += record
finally:
reader.close()
for key in writers:
writers[key].close()
logger.info(
"Processed a total of {0} records from {1} and found {2} read keys".format(
count, ibase, len(writers)
)
)
return ({key: writers[key].reporter.to_dict() for key in writers}, count)
def main_handler(args):
"""Main entrypoint to pass either for single end parsing or
paired end parsing.
"""
logger = get_logger('handler')
if args.fastq_b:
assert args.fastq_a != args.fastq_b
logger.info('Running in paired mode')
main_paired(args)
else:
logger.info("Running in single mode")
main_single(args)
def main(args=None):
"""The main method for gdc-fastq-splitter"""
start = time.time()
logger = get_logger('gdc-fastq-splitter')
parser = argparse.ArgumentParser()
parser.add_argument('--version', action='version', version=VERSION)
parser.add_argument('-o', '--output-prefix', required=True, type=str,
help='The output prefix to use for output files.')
parser.add_argument('fastq_a', help='Fastq file to process')
parser.add_argument('fastq_b', nargs='?', help='If paired, the mate fastq file to process')
options = parser.parse_args(args=args)
main_handler(options)
logger.info("Finished. Took {0:.2f} seconds".format(time.time() - start))
def main_single(args):
"""
Main handler for single fastq files. It will check the returned metrics
to make sure everything matches.
"""
logger = get_logger('single_handler')
results = process_fastq(args.fastq_a, args.output_prefix)
logger.info("Finished splitting; Validating results")
input_total = results[1]
data = results[0]
counts = 0
for key in data:
fil = data[key]['metadata']['fastq_filename']
ct = data[key]['metadata']['record_count']
counts += ct
if counts != input_total:
msg = "The number of records input and output doesn't match! ({0}, {1})".format(
input_total, counts)
logger.error(msg)
raise ValueError(msg)
def main(args=None):
"""The main method for gdc-fastq-splitter"""
start = time.time()
logger = get_logger("gdc-fastq-splitter")
parser = argparse.ArgumentParser()
parser.add_argument("--version", action="version", version=VERSION)
parser.add_argument(
"-o",
"--output-prefix",
required=True,
type=str,
help="The output prefix to use for output files.",
)
parser.add_argument("fastq_a", help="Fastq file to process")
parser.add_argument("fastq_b",
nargs="?",
help="If paired, the mate fastq file to process")
options = parser.parse_args(args=args)
main_handler(options)
logger.info("Finished. Took {0:.2f} seconds".format(time.time() - start))
def main_paired(args):
"""
Main handler for paired fastq files. This will use 2 processors to parse
each fastq separately in parallel and aggregate the returned metrics to
make sure everything matches.
"""
logger = get_logger('paired_handler')
pool = multiprocessing.Pool(2)
tasks = [(i, args.output_prefix) for i in [args.fastq_a, args.fastq_b]]
results = pool.map(do_process, tasks)
logger.info("Finished splitting; Validating results")
# Validate the results
result_a, result_b = results
result_a_input_total = result_a[1]
result_b_input_total = result_b[1]
if result_a_input_total != result_b_input_total:
msg = "The input files had different number of records! ({0}, {1})".format(
result_a_input_total, result_b_input_total)
logger.error(msg)
raise ValueError(msg)
result_a_data = result_a[0]
result_b_data = result_b[0]
if len(result_a_data) != len(result_b_data):
msg = "The input files had different number of read keys! ({0}, {1})".format(
len(result_a_data), len(result_b_data))
logger.error(msg)
raise ValueError(msg)
a_keys = list(result_a_data.keys())
b_keys = list(result_b_data.keys())
sdiff = set(a_keys).symmetric_difference(set(b_keys))
if sdiff:
msg = "These read keys were not found in both files: {0}".format(
",".join(list(sdiff)))
logger.error(msg)
raise ValueError(msg)
written_a = 0
written_b = 0
for key in a_keys:
a_fil = result_a_data[key]['metadata']['fastq_filename']
a_ct = result_a_data[key]['metadata']['record_count']
b_fil = result_b_data[key]['metadata']['fastq_filename']
b_ct = result_b_data[key]['metadata']['record_count']
if a_ct != b_ct:
msg = "The output files ({0}, {1}) have different totals! ({2}, {3})".format(
a_fil, b_fil, a_ct, b_ct)
logger.error(msg)
raise ValueError(msg)
written_a += a_ct
written_b += b_ct
if written_a != result_a_input_total:
msg = "The number of records input and output doesn't match! ({0}, {1})".format(
result_a_input_total, written_a)
logger.error(msg)
raise ValueError(msg)
if written_b != result_b_input_total:
msg = "The number of records input and output doesn't match! ({0}, {1})".format(
result_b_input_total, written_b)
logger.error(msg)
raise ValueError(msg)
