python26

#!/usr/bin/env python
# -*- coding: utf-8 -*-

import os
import sys
import re
from Bio import SeqIO
from Bio.Seq import Seq

in1=sys.argv[1] # the file of fastq
id1 = sys.argv[2] # the file of id
ou1 = sys.argv[3] # the fastq of triming id

idlist = []
with open(id1,'r') as idi:
    idl=idi.readlines()
    for idli in idl:
        idlci=idli.strip().split('\n')
        idlc=str(idlci[0])
        idlist.append(idlc)
print(idlist)

outc=open(ou1,'w')
for h in SeqIO.parse(in1,"fastq"):
    idc=h.id
    print(str(idc))
    seq=h.seq
    if str(idc) in idlist:
        outc.write(">"+str(idc)+"\n"+str(seq)+"\n")