356286.py

from argparse import ArgumentParser
from Bio import SeqIO
from collections import Counter, defaultdict
import gzip


def main():
    args = get_args()
    primers = defaultdict(int)
    for pattern in args.pattern:
        for read in SeqIO.parse(gzip.open(args.fastq, 'rt'), "fastq"):
            primer = get_pattern(str(read.seq), pattern, length=22)
            if primer:
                primers[primer] += 1
        for sequence, number in Counter(primers).most_common(n=20):
            print("{}\t{}x".format(sequence, number))


def get_pattern(seq, pattern, length):
    if pattern in seq:
        pos = seq.index(pattern)
        return seq[pos - (length - len(pattern)): pos + len(pattern)]


def get_args():
    parser = ArgumentParser(description="Get primers based on a fastq www.biostars.org/p/356286")
    parser.add_argument("--pattern", help="pattern(s) to search for", nargs="*", required=True)
    parser.add_argument("--fastq", help="gzip compressed fastq file", required=True)
    return parser.parse_args()


if __name__ == '__main__':
    main()