Syncs a barcode.fastq file to the joined.fastq file produce by ea-util's fastq-join script.

fastq-barcode.pl

#!/usr/bin/perl
#
# ---------------------------------------- #
#   Daniel Smith - October 1st, 2012       #
#   Argonne National Laboratory            #
#   Creative Commons License BY-SA 3.0     #
# ---------------------------------------- #
#

use strict;
use warnings;

my $USAGE = <<EOF;

USAGE: $0 barcodes.fastq joined_reads.fastq > barcode_subset.fastq

This script is designed to complement ea-util's fastq-join script.
Given three fastq-formatted files containing the forward, reverse, and barcode
reads, a joined and corresponding barcode file can be generated via:

fastq-join forward.fastq reverse.fastq -o out.%.fastq
$0 barcodes.fastq out.join.fastq > out.barcodes.fastq

The purpose of $0 is to remove entries from barcodes.fastq which
no longer have a corresponding read in out.join.fastq. 

EOF


my $barcode_file = shift || die ($USAGE);
my $joined_file  = shift || die ($USAGE);

die $USAGE unless (-r $barcode_file && -r $joined_file);

open (BARCODES, $barcode_file) or die ("$!\n");
open (READS,    $joined_file)  or die ("$!\n");
while (my $header = <READS>) {
	my $line  = <READS>;
	   $line  = <READS>;
	   $line  = <READS>;
	
	my ($bc1, $bc2, $bc3, $bc4) = map("", 1..4);
	while ($bc1 ne $header) {
		exit if (eof(BARCODES));
		
		$bc1 = <BARCODES>;
		$bc2 = <BARCODES>;
		$bc3 = <BARCODES>;
		$bc4 = <BARCODES>;
	}
	
	print $bc1, $bc2, $bc3, $bc4;
}
close READS;
close BARCODES;

@dansmith01

A little perplexing, but this current script does not pull the barcodes correctly. I end up with an empty barcodes join.fastq when I install and run it. Your older script when it was being hosted by dropbox years seems to run fine (we installed from an older computer)? I just was wondering why? It's similar to the problem the previous posters issue. We had an older version of your perl script that we reinstalled and this script was able to pull the barcodes out.