bwa_split_indiv

#!/usr/bin/perl
#
#Copyright (C) 2013- The University of Notre Dame
#This software is distributed under the GNU General Public License.
#See the file COPYING for details.
#
#Revised: Nick Hazekamp
#Date: 12/02/2013
#
#Purpose: Split a FASTQ file into smaller files determined by the number of sequences input

use strict;
use Symbol;

if ($#ARGV != 1) {
	print "Usage: perl bwa_split_indiv <barcode->individual file> <fastq file>\n";
	exit 1;
}

my $prog_file = shift;
my $file = shift;

my %progs = ();
my $output;

my $numargs = $#ARGV + 1;

open(PROG, $prog_file);
while (my $line = <PROG>) {
	my @line_array = split(' ',$line);
	my $file = $line_array[1];
	my $name = gensym;
	open( $name, ">$file.fq");
	$progs{ $line_array[0] } = $name;
	$output = $file;
}
close(PROG);

#Open input file
open(INPUT, $file);

while (my $line = <INPUT>) {
	chomp $line;
	#FASTQ files begin sequence with '@' character
	#If line begins with '@' then it is a new sequence and has 3 lines in between
	if ($line =~ /^[@]/){
		my @matches = ($line =~ /(index_[^_]+_[^_]+)/);
		$output = $progs{ $matches[0] };
		if ($output){
			print $output $line;
			print $output "\n";
		}
	}
	#place all other lines in FASTQ file under same sequence
	else {
		if ($output){
			print $output $line;
			print $output "\n";
		}
	}
}
close(INPUT);

while ( my ($key, $value) = each(%progs) ) {
	close($value);
}