rename SmartSeq3 script

#!/usr/bin/perl

#########################################

#                                       #

#     Written by Kai Battenberg         #

#     Plant Symbiosis Research Team     #

#                                       #

#########################################

use strict;

use warnings;

use Getopt::Long;

#####SCRIPT DESCRIPTION#####

#Script "cat_fastq.pl" given a reference file, and a list of fastq files, concatenates all the additive sequences to add in front of each reference read.

###########

#####Options#####

#setting the default values.

my $ref_fastq = "";

my @additives = ();

my $concatenated_fastq = "cat.fastq";

my $out_dir = "";

#making the options into external arguments.

GetOptions (

	'ref_fastq=s' => \$ref_fastq,

	'additives=s' => \@additives,

	'out_dir=s' => \$out_dir

	);

#Checking options

if (!$ref_fastq) {

	die "USAGE: option --ref_fastq <Reference.fastq> is required.\n";

}

elsif (scalar @additives < 1) {

	die "USAGE: option --additives <additional.fastq> is required.\n";

}

elsif (!$out_dir) {

	die "USAGE: option --out_dir <OUTPUT_DIRECTORY> is required.\n";

}

$concatenated_fastq = $out_dir."/".$concatenated_fastq;

$concatenated_fastq =~ s/\/\//\//;

##########

#####MAIN#####

#read in additive data

my %additives_seq;

my %additives_q;

foreach my $file (@additives) {

	my $readcount = 0;

	open (ADD, "<", $file) or die "cannot open $file.\n";

	while (my $line = <ADD>) {

		$readcount++;

		my $head = $line;

		my $seq = <ADD>;

		my $plus = <ADD>;

		my $q = <ADD>;

		chomp $seq;

		chomp $q;

		#save additive data

		if (!$additives_seq{$readcount}) {

			$additives_seq{$readcount} = $seq;

		}

		else {

			$additives_seq{$readcount} = $additives_seq{$readcount}.$seq;

		}

		if (!$additives_q{$readcount}) {

			$additives_q{$readcount} = $q;

		}

		else {

			$additives_q{$readcount} = $additives_q{$readcount}.$q;

		}

	}

	close (ADD);

}

#add data to reference

my $ref_readcount = 0;

open (REF, "<", $ref_fastq) or die "cannot open $ref_fastq.\n";

open (CAT, ">", $concatenated_fastq) or die "cannot open $concatenated_fastq.\n";

while (my $line = <REF>) {

	$ref_readcount++;

	my $head = $line;

	my $seq = <REF>;

	my $plus = <REF>;

	my $q = <REF>;

	my $new_seq = $additives_seq{$ref_readcount}.$seq;

	my $new_q = $additives_q{$ref_readcount}.$q;

	print CAT "$head";

	print CAT "$new_seq";

	print CAT "$plus";

	print CAT "$new_q";

}

close (REF);

close (CAT);

##########