Script for alphabetical sorting FASTQ files by their identifier. Example: `bzcat unsorted.fq.bz2 | sortfq | bzip2 > sorted.fq.bz2`

sortfq

#!/usr/bin/env perl

# Martin A. Hansen (mail@maasha.dk), September 2011

use strict;
use warnings;

use IPC::Open2;
use File::Which;

print STDERR "Usage: sortfq < unsorted.fq > sorted.fq\n\n" and exit if -t STDIN;

my $exe = which("psort") ? "psort" : "sort";

open2(\*IN, \*OUT, qq(paste - - - - | $exe -k1,1 -t " " | tr "\t" "\n")); 

while (<>) {
    print OUT $_;
}

close OUT;

while (<IN>) {
    print;
}

close IN;