post demultiplexing script as example

[ctb]

see below:

#! /usr/bin/env python
from __future__ import print_function
import screed
import sys
import argparse

p = argparse.ArgumentParser()
p.add_argument('r1_file')
p.add_argument('r2_file')
p.add_argument('code_r1')
p.add_argument('code_r2')
args = p.parse_args()

for record1, record2 in zip(screed.open(args.r1_file),
                            screed.open(args.r2_file)):
    if record1.sequence[8:].startswith(args.code_r1) and \
       record2.sequence[0:].startswith(args.code_r2):
       
       print('@{}\n{}\n+\n{}'.format(record1.name, record1.sequence,
                                     record1.quality))
       print('@{}\n{}\n+\n{}'.format(record2.name, record2.sequence,
                                     record2.quality))