Script to compare two fastq files, print labels that do not match, and tests for sequence/quality lengths that are different (useful in cases where one suspects index reads and other reads do not have matching labels). Made to work with CASAVA 1.8.0 and later, might fail on earlier versions.Usage: python compare_fastq_labels.py fastq1_fp fastq2_fp

compare_fastq_labels.py

#!/usr/bin/env python

# Modified from Greg Caporaso's code in qiime/split_libraries_fastq.py

# Usage:  python compare_fastq_labels.py fastq1_fp fastq2_fp

from itertools import izip
from sys import argv

from cogent.parse.fastq import MinimalFastqParser

header_index = 0
sequence_index = 1
quality_index = 2

read1 = open(argv[1], "U")
read2 = open(argv[2], "U")

def check_header_match_180_or_later(header1,header2):
    """ Confirm headers are compatible in CASAVA 1.8.0 or later
        
        These contain information on the read number, so can differ
    """
    header1 = header1.split(':')
    header2 = header2.split(':')
    for e1,e2 in zip(header1,header2):
        if e1.split(' ')[0] != e2.split(' ')[0]:
            return False
    
    return True

print "Printing labels that do not match before space character:"
mismatched_labels_found = False

for read1_data,read2_data in izip(MinimalFastqParser(read1,strict=False),
                                  MinimalFastqParser(read2,strict=False)):

    if not check_header_match_180_or_later(read1_data[header_index], read2_data[header_index]):
        print "Mismatched labels: %s, %s" % (read1_data[header_index], read2_data[header_index])
        mismatched_labels_found = True
    if not (len(read1_data[sequence_index]) == len(read1_data[quality_index])):
        print "Sequence and quality score lengths do not match for read 1 label %s " % read1_data[header_index]
    if not (len(read2_data[sequence_index]) == len(read2_data[quality_index])):
        print "Sequence and quality score lengths do not match for read 2 label %s " % read2_data[header_index]
        
if not mismatched_labels_found:
    print "No mismatched labels found."