fastq_reduce

#!/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.
#
#Programmer: Brian Kachmarck
#Date: 7/28/2009
#
#Revised: Nick Hazekamp
#Date: 12/02/2013
#
#Purpose: Split a FASTQ file into smaller files determined by the number of sequences input

use strict;


my $numargs = $#ARGV + 1;

my $file = $ARGV[0];

my $num_reads= $ARGV[1];

my $num_outputs = 0;
my $line_count=0;

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

my $read_count = 0;
open (OUTPUT,">$file.$num_outputs");
$num_outputs++;
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 =~ /^[@]/ and $line_count % 4 ==0){
		#Check if the new sequence should be placed in a new file, otherwise place it in same file
		if ($read_count == $num_reads){
			close(OUTPUT);
			open(OUTPUT, ">$file.$num_outputs");
			print OUTPUT $line;
			print OUTPUT "\n";
			$num_outputs++;
			$read_count = 1;
		}
		else{
			print OUTPUT $line;
			print OUTPUT "\n";
			$read_count++;
		}
	}
	#place all other lines in FASTQ file under same sequence
	else {
		print OUTPUT $line;
		print OUTPUT "\n";
	}

	$line_count++;
}
print $num_outputs;

close(INPUT);