PERL: Union Gene Model

unionGeneModelforTAIR10.pl

#!/usr/bin/perl -w 
use strict;

# Notice: 
# BED annotation should be sorted by the GeneID or GeneName ahead
# otherwise duplication in output 
my $inBed = shift || die $!;
my $outUnion = shift || die $!;

open OUT, "> $outUnion";
open IN, $inBed;

my $lastID = "";
while (<IN>) {
	chomp;
	my $info = $_;
	my @info = split /\t/, $info;
	my $id = $info[3]; 
	# AT1G01010.1 -> AT1G01010
	$id =~ s/(\w+)\.(\d+)/$1/g ;
	if ($id ne $lastID) {
			# grep loci, mergeBed, awk to std BED6
			# print $id . "\n";
			print OUT `grep $id $inBed | mergeBed -i stdin -s -nms | awk '{print \$1,\$2,\$3,\$4,0,\$5}' OFS="\t" `;
			$lastID = $id;
		}	
	else {
		next ;
	}
}