#!/usr/bin/perl -w

# The program split_fastq_paired_reads.pl splits a fastq files with paired reads into two files containing first and second reads of each pair, respectively.
# Copyright (C) 2012 Minou Nowrousian

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details (http://www.gnu.org/licenses/).


use strict;
use warnings;


unless (@ARGV == 1) {
	die("program usage: split_fastq_paired_reads.pl paired_read_file.fastq\n");
}

unless (-e $ARGV[0]) {
	die("Can't open file $ARGV[0]: $!");
}

print "Splitting fastq file $ARGV[0] into two fastq files.\nAssuming read order pair1_read1, pair1_read2, pair2_read1, pair2_read2 etc.\n";


open INPUTFILE, "< $ARGV[0]" or die "Kann Datei nicht oeffnen: $!";

my $outfile1 = $ARGV[0] . "_read1.fastq";
	
my $outfile2 = $ARGV[0] . "_read2.fastq";

open OUTFILE1, ">> $outfile1" or die "Kann Datei $outfile1 nicht oeffnen: $!";
open OUTFILE2, ">> $outfile2" or die "Kann Datei $outfile2 nicht oeffnen: $!";
	
while (<INPUTFILE>) {
	
	my $line1_1 = $_;

	if ($line1_1 !~ /^@/) {
		print "first line of read does not start with @ at read $line1_1\n";
	}

	my $line1_2 = <INPUTFILE>;
	my $line1_3 = <INPUTFILE>;
	my $line1_4 = <INPUTFILE>;
	
	my $line2_1 = <INPUTFILE>;

	if ($line2_1 !~ /^@/) {
		print "first line of read does not start with @ at read $line2_1\n";
	}

	my $line2_2 = <INPUTFILE>;
	my $line2_3 = <INPUTFILE>;
	my $line2_4 = <INPUTFILE>;

	print OUTFILE1 $line1_1, $line1_2, $line1_3, $line1_4;
	print OUTFILE2 $line2_1, $line2_2, $line2_3, $line2_4;
			
}
		
close INPUTFILE;
close OUTFILE1;
close OUTFILE2;