| #!/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() | |