check_interleaved_fastq

#!/usr/bin/env python
# encoding: utf-8

import sys
import argparse

def interface():
    parser = argparse.ArgumentParser()

    parser.add_argument('INPUT',
                        type=argparse.FileType('r'),
                        default=sys.stdin,
                        nargs='?',
                        help='interleaved reads.')

    parser.add_argument('GOOD_OUTPUT',
                        type=argparse.FileType('w'),
                        default=sys.stdout,
                        nargs='?',
                        help='Correctly Interleaved reads')

    parser.add_argument('BAD_OUTPUT',
                        type=argparse.FileType('w'),
                        default=sys.stderr,
                        nargs='?',
                        help='Non Interleaved reads')

    args = parser.parse_args()
    return args


def process_reads(args):
    
    inp = args.INPUT
    fout = args.GOOD_OUTPUT
    ferr = args.BAD_OUTPUT
    
    # USING A WHILE LOOP MAKES THIS SUPER FAST
    # Details here: 
    #   http://effbot.org/zone/readline-performance.htm

    forward = ["","","","",""]
    name, strand = "", ""
    
    while 1: 

        # process the first file
        idstring = inp.readline()
        if not idstring: break
        if "/1" in idstring or "/2" in idstring:
            name, strand = idstring.rstrip().split("/")
        else:
            name, strand = idstring.split(" ", 2)
            strand = strand.split(":")[0]
        seq = inp.readline()
        plus = inp.readline()
        quals = inp.readline()
        if strand == "1":
            if forward[0] != "":
                ferr.write(forward[1]+forward[2]+forward[3]+forward[4])
            forward = [name, idstring, seq, plus, quals]
        elif name == forward[0]:
            fout.write(forward[1]+forward[2]+forward[3]+forward[4])
            fout.write(idstring+seq+plus+quals)
            forward = ["","","","",""]
        else:
            ferr.write(forward[1]+forward[2]+forward[3]+forward[4])
            forward = ["","","","",""]
    inp.close()
    fout.close()
    ferr.close()
    return 0

if __name__ == '__main__':
    args = interface()
    process_reads(args)