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from argparse import ArgumentParser
from Bio import SeqIO
import gzip
def main():
args = get_args()
for record in SeqIO.parse(gzip.open(args.fastq, 'rt'), "fastq"):
print(record[-args.bases_from_end:].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("--bases_from_end",
help="get a fragment of each read N bp from end",
default=100,
type=int)
return parser.parse_args()
if __name__ == '__main__':
main()
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