deinterlacer.sh

#!/usr/bin/env python3

import argparse
import os
import sys

# Deinterlace an interlaced fastq file 
# (modified from iamdelf/deinterlace)

# usage: 
# cat interlaced_input.fastq | deinterlacer.sh output_R1.fq output_R2.fq

def main():
    parser = argparse.ArgumentParser(description='Splits an interleaved FASTQ (input in STDIN) into first and second read files')
    parser.add_argument('first')
    parser.add_argument('second')
    args = parser.parse_args()

    pipeForward = os.open( os.path.join(os.getcwd(),args.first) , os.O_WRONLY|os.O_CREAT|os.O_EXCL)
    pipeReverse = os.open( os.path.join(os.getcwd(),args.second) , os.O_WRONLY|os.O_CREAT|os.O_EXCL)

    i = 0
    forward = True
    for line in sys.stdin:
        if forward:
            os.write(pipeForward, line.encode())
        else:
            os.write(pipeReverse, line.encode())
        i += 1
        if i == 4:
            forward = not forward
            i = 0
    
if __name__ == '__main__':
    main()