python38

#!/usr/bin/env python
##coding=utf-8

import re
import os
import sys
import argparse
import gzip

parser = argparse.ArgumentParser(description="pipeline")
parser.add_argument('-i', '--input', help = 'the pathway of the input fastq file ', required = True)
parser.add_argument('-id', '--input_id', help = 'the pathway of the input id file ', required = True)
parser.add_argument('-o', '--output', help = 'the pathway of the output vcf file,filter vcf', required = True)
argv = vars(parser.parse_args())
ifile = os.path.abspath(argv['input'].strip())
ofile = os.path.abspath(argv['output'].strip())
idf = os.path.abspath(argv['input_id'].strip())

def creatlist(inputfile):
    idlist=[]
    with open(inputfile,'rb') as v:
        for vi in v:
            vic = vi.strip().split('\n')
            idlist.append(str(vic[0]))
    return idlist

def trimfq(inputfile,outfile,idList):
    oc=open(outfile,'w')
    with gzip.open(inputfile,'rb') as v:
        i=0
        idn=-1
        for vi in v:
            i=i+1
            vic = vi.strip().split('\n')
            vicon=vic[0]
            if str(vicon).startswith('@'):
                vcid=str(vicon).replace('@','')
                if vcid in idList:
                    print("vcid : "+str(vcid))
                    idn=i
                    idr=vcid
            elif int(i)==idn+1:
                idseq=str(vicon)
                oc.write(">"+str(idr)+"\n"+str(idseq)+"\n")
    oc.close

idL=creatlist(idf)
trimfq(ifile,ofile,idL)