woland-bed.pl

#####################################################################################################################################
## WOLAND Beta 1.01 (09-30-2017)
## woland-bed.pl
##
## WOLAND is a multiplatform tool to analyze point mutation patterns using resequencing data from any organism or cell. 
##
## For more details please read README file.
##
######################################################################################################################################

#! /usr/bin/perl
use List::Util qw(sum); #module for sum of chromosome coordinates
use List::MoreUtils qw(uniq);
use strict;
use warnings;
use Getopt::ArgParse;

our $REVISION = '$Revision:  $';
our $DATE =	'$Date: 2017-09-30 00:11:04 -0800 (Sat,  30 Sep 2017) $';  
our $AUTHOR =	'$Author: Tiago A. de Souza <tiagoantonio@gmail.com> $';

our (@chrbed,@pos1,@pos2, @sumlength,@uniquechr);
our $bedfile;

sub parse_bedfile{ # loading bed file
	my $args = $_[0];
	# $bedfile = $ARGV[0];
	$bedfile = $args->bed_file;
	open (BEDFILE, $bedfile);
	my @bedfilearray=<BEDFILE>;
	close (BEDFILE);

	my $rawbedline;

	foreach $rawbedline (@bedfilearray){
		my @i = split (/\t/, $rawbedline);
		chomp (@i);
		push (@chrbed, "$i[0]");
		push (@pos1, $i[1]);
		push (@pos2, $i[2]);
	}
	shift(@chrbed);
	@uniquechr = uniq @chrbed; #unique chromosome names
	
	for my $i (0..$#uniquechr){
		&calculate_length($uniquechr[$i]);
	}
}

sub calculate_length{ #absolute subtraction of pos values
	my @length;
	for my $i(0..$#chrbed){
		if($chrbed[$i] eq "$_[0]"){
			$length[$i]=abs($pos2[$i]-$pos1[$i]);
		}
		if($chrbed[$i] ne "$_[0]"){
			$length[$i]=0;
		}
	}
	push (@sumlength, sum(@length));
}

my $ap = Getopt::ArgParse->new_parser(
	prog => 'woland-bed.pl',
	description => 'WOLAND is a multiplatform tool to analyze point mutation patterns using resequencing SNV data. 
	Use woland-bed.pl to calculate nucleotide length using a .BED coordinate file as input and to build <chromosome_length_profile> for other woland scripts.For more details please read README',
	epilog => 'If you used Woland in your research, we would appreciate your citation:
	de Souza TA, Defelicibus A, Menck CF',
 );

$ap->add_arg(
	'--bed-file',
	'-b',
	required => 1,
	help => 'BED-formatted file of targeted-sequencing regions');

my $args = $ap->parse_args();

## main warning
# unless ($#ARGV==0){
# 	die "\nERROR : Incorrect number of arguments - Usage: $0 <file.bed> \n\n";	
# }
unless (-r -e -f $args->bed_file){
    die sprintf("\nERROR: %s not exists or is not readable or not properly formatted. Please check file.\n\n",
    	$args->bed_file);
}

&parse_bedfile($args);

open (PROFILE, ">>woland-bed-profile-$bedfile"); # printing profile file
for my $i (0..$#uniquechr){
	print PROFILE "$uniquechr[$i]\t";
	if ($sumlength[$i] ne 0){
		print PROFILE "$sumlength[$i]\n";
	}
	else{
		print PROFILE "\1\n";
	}
}
close(PROFILE);

exit;