python8

# -*- coding: utf-8 -*-

import os
import sys
import gzip
from Bio import SeqIO

inputfile = sys.argv[1]
outfile = sys.argv[2]
content = sys.argv[3]

outcont = open(outfile,"w")
count = 0

for seq_recode in SeqIO.parse(inputfile,"fastq"):
    print(seq_recode)
    read2file = seq_recode.seq
    if str(content) in read2file:
        lenght = str(read2file).find(content)
        strseq = str(read2file)[0:int(lenght)]
        print(strseq)