#! /usr/bin/perl

use strict;
use warnings;

my @d1 = qw{
        CLS_S3_Contig2721-139_168
        CLS_S3_Contig2722-375_390
        CLS_S3_Contig2725-323_362
        CLS_S3_Contig2725-455_480
        CLS_S3_Contig2728-117_144
        CLS_S3_Contig2728-437_472
        CLS_S3_Contig2729-119_130
        CLS_S3_Contig2729-163_220
        CLS_S3_Contig2730-181_202
        CLS_S3_Contig2730-361_384
        CLS_S3_Contig2731-824_843
        CLS_S3_Contig2731-1150_1201
        CLS_S3_Contig2735-571_636
        CLS_S3_Contig2735-677_710
        CLS_S3_Contig2735-775_810
    };

my @d2 = qw{
        CLS_S3_Contig2721-142_169
        CLS_S3_Contig6525-509_514
        CLS_S3_Contig6525-493_502
        CLS_S3_Contig6525-503_508
        CLS_S3_Contig2977-365_376
        CLS_S3_Contig2977-77_82
        CLS_S3_Contig2977-83_90
        CLS_S3_Contig4978-271_274
        CLS_S3_Contig4978-385_388
        CLS_S3_Contig2730-365_389
    };

{
    my %d_one = ();
    my %d_two = ();

    for( @d1 ) {
        my ($key, $start, $end) = $_ =~ /(.*)-(\d+)_(\d+)/;
        push @{ $d_one{$key} }, { 'start' => $start, 'end' => $end };
    }

    for( @d2 ) {
        my ($key, $start, $end) = $_ =~ /(.*)-(\d+)_(\d+)/;
        push @{ $d_two{$key} }, { 'start' => $start, 'end' => $end };    
    }

    use Data::Dumper;
    
    print Dumper(\%d_one, \%d_two);

    print "Genename(file1)\t\tstart\tend\t**\tGenename(file2)\t\tstart\tend\n\n";

    foreach my $key_one ( keys %d_one ) {
        
        if( $d_two{$key_one} ) { # We found a matching key!
            
            foreach my $limits_one ( @{ $d_one{$key_one} } ) {
                
                foreach my $limits_two ( @{ $d_two{$key_one} } ) {
                    
                    if( $limits_two->{'start'} >= $limits_one->{'start'} &&
                        $limits_two->{'start'} <= $limits_one->{'end'} ) {
                            
                            print "$key_one\t$limits_one->{'start'}\t$limits_one->{'end'}"
                                . "\t**\t"
                                . "$key_one\t$limits_two->{'start'}\t$limits_two->{'end'}\n";                                
                        }
                }
            }            
        }
    }
}