colline2yml_AL.pl

use strict;
use warnings;
use AlignDB::IntSpan;

my %genes;
my %genee;
open GFF,"<",$ARGV[0];
while(<GFF>){
	chomp;
	my @tmp = split("\t",$_);
	$genes{$tmp[1]} = $tmp[2];
	$genee{$tmp[1]} = $tmp[3];
}
close GFF;

open COLL,"<",$ARGV[1];
my @collin = <COLL>;
close COLL;

print"---\n";

my %chr = ( 1=>"I", 2=>"II", 3=>"III", 4=>"IV", 5=>"V" );

my @seg;
foreach(1..5){
	$seg[$_] = AlignDB::IntSpan->new;
}

my $i = 0;
while($i <= $#collin){
	if($collin[$i] =~ /## Alignment (\w+)/){
		my $ore;
		if($collin[$i] =~ /plus/){
			$ore = 1;
		}else{
			$ore = -1;
		}
		$i++;
		my @at;
		until(($i > $#collin) or ($collin[$i] =~ /## Alignment/)){
			my @tmp = split("\t",$collin[$i]);
			push(@at,$tmp[2]);
			$i++;
		}
		$i--;
        	$at[0] =~ /AT([1-5])G/;
        	my $chr = $1;
		if($ore == 1){
			my $s = $genes{$at[0]} - 2000;
		        my $e = $genee{$at[-1]} + 2000;
        		$seg[$chr]->add_pair($s,$e);
		}else{
			my $s = $genes{$at[-1]} - 2000;
	        	my $e = $genee{$at[0]} + 2000;
            		$seg[$chr]->add_pair($s,$e);
		}
	}
	$i++;
}

foreach(1..5){
    print"$chr{$_}: $seg[$_]\n";
}