#!/usr/bin/python
import sys
import Bio
from Bio import SeqIO
import gzip
from glob import glob
import re

f = sys.argv[1]
R1 = gzip.open(f, "rt")
R2 = gzip.open(re.sub("_R1_001.fastq.gz", "_R2_001.fastq.gz", f), "rt")
out = gzip.open(re.sub("_S\\d+_L003_R1_001.fastq.gz", ".fastq.gz", f), "wt")

fq1 = SeqIO.parse(R1, "fastq")
fq2 = SeqIO.parse(R2, "fastq")
for (r1, r2) in zip(fq1, fq2):
    name = str(r1.name)
    umi = str(r2.seq)
    r1.description = name+'_'+umi
    r1.name = name+'_'+umi
    r1.id = name+'_'+umi
    out.write(r1.format("fastq"))

R1.close()
R2.close()
out.close()