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from argparse import ArgumentParser
from Bio import SeqIO
import gzip
from dateutil.parser import parse as dparse
def main():
args = get_args()
for record in SeqIO.parse(gzip.open(args.fastq, 'rt'), "fastq"):
if filter_time(record.description, args.time_from, args.time_to):
print(record.format("fastq"), end="")
def get_args():
parser = ArgumentParser(description="Filter nanopore data based on time")
parser.add_argument("fastq", help="input gzip compressed fastq file")
parser.add_argument("--time_from", help="filtering reads after this", required=True)
parser.add_argument("--time_to", help="filtering reads before this", required=True)
return parser.parse_args()
def filter_time(descr, tfrom, tto):
"runid=2582f1be82a0c29a01c4c852b672559257416ff6 read=12 ch=2153 start_time=2017-10-13T11:54:09Z"
time = dparse([i for i in descr.split() if i.startswith('start_time')][0].split('=')[1])
if dparse(tfrom) <= time <= dparse(tto):
return True
else:
return False
if __name__ == '__main__':
main()
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