script to fill mock UMIs for non-UMI techniques

#!/usr/bin/perl

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

#                                       #

#     Written by Kai Battenberg         #

#     Plant Symbiosis Research Team     #

#                                       #

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

use strict;

use warnings;

use Getopt::Long;

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

#Script "add_mock_UMI.pl" given a FASTQ file, starting position, and desired UMI length, generates a new FASTQ file with a mock UMI inserted.

###########

######Options#####

my $fastq_in = "";

my $fastq_out = "mock_UMI.fastq";

my $head_length = ""; #number of characters to have before insertion of mock UMI.

my $umi_length = ""; #length of desired UMI

##########

#####Checking Options#####

#making the options into external arguments.

GetOptions (

	'fastq=s' => \$fastq_in,

	'head_length=s' => \$head_length,

	'umi_length=s' => \$umi_length

	);

#checking for required options.

if (!$fastq_in) {

	die "USAGE: option --fastq <FASTQ FILE> is required.\n";

}

elsif (!$head_length) {

	die "USAGE: option --head_length <INTEGER> is required.\n";

}

elsif (!$umi_length) {

	die "USAGE: option --umi_length <INTEGER> is required.\n";

}

#checking head length

if ( $head_length !~ /^-?\d+\.?\d*$/ ) {

	die "Error: option --head_length needs to be numeric\n";

}

elsif ( $head_length < 0 || $head_length !~ /^-?\d+$/ ) {

	die "Error: option --head_length needs to be an integer 0 or greater\n";

}

#checking umi length

if ( $umi_length !~ /^-?\d+\.?\d*$/ ) {

	die "Error: option --umi_length needs to be numeric\n";

}

elsif ( $head_length < 1 || $head_length !~ /^-?\d+$/ ) {

	die "Error: option --umi_length needs to be an integer 0 or greater\n";

}

##########

#####Main#####

my %nucleotide = (

	'00' => "A",

	'01' => "C",

	'10' => "G",

	'11' => "T"

);

my $insert_q = "I" x $umi_length;

my $read_count = -1;

open (IN, "<", $fastq_in) or die "cannot open $fastq_in.\n";

open (OUT, ">", $fastq_out) or die "cannot open $fastq_out.\n";

while (my $line = <IN>) {

	$read_count++;

	#get binary read count

	my $binary = sprintf ("%b", $read_count);

	$binary = (0 x (2 * $umi_length)).$binary;

	$binary = reverse(substr (reverse ($binary), 0, 2 * $umi_length));

	my @binary = ( $binary =~ m/../g );

	#get mock UMI

	my $mock_umi = "";

	foreach my $character (@binary) {

		$mock_umi = $mock_umi.$nucleotide{$character};

	}

	#get data from FASTQ file

	my $header = $line;

	chomp $header;

	my $seq = <IN>;

	chomp $seq;

	my $plus = <IN>;

	my $q = <IN>;

	chomp $q;

	#insert 

	my $seq_head = substr($seq, 0, $head_length);

	my $seq_tail = reverse(substr (reverse ($seq), 0, length($seq) - $head_length));

	my $q_head = substr($q, 0, $head_length);

	my $q_tail = reverse(substr (reverse ($q), 0, length($q) - $head_length));

	print OUT "$header\n";

	print OUT "$seq_head$mock_umi$seq_tail\n";

	print OUT "$plus";

	print OUT "$q_head$insert_q$q_tail\n";

}

close (IN);

close (OUT);

##########

__END__