Thank you very much for your nice code. I am just wondering if it works if there are redundant keys. As you can see in my input files the gene names may repeat over and over. This will be in jeopardy of key concept of hash in perl?

thanks again

Yes, that would ruin my approach. In this case I would introduce and array to the hash. It complicates things, but only a little bit :-)

Update: Corrected a wrong hash key in the printout.

Update2: Removed incorrect next statement.

Here is the modified version. The algo can get heavy if the data is large, so maybe wiser monks could help a bit here?

#! /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";                                
                        }
                }
            }            
        }
    }
}
[download]

Note, write test cases for this or test otherwise extensively. Below is the current output of my script:

cpt2jmo@phantom:~/misc$ ./2_hashes_with_arrays.pl
$VAR1 = {
          'CLS_S3_Contig2722' => [
                                   {
                                     'end' => '390',
                                     'start' => '375'
                                   }
                                 ],
          'CLS_S3_Contig2725' => [
                                   {
                                     'end' => '362',
                                     'start' => '323'
                                   },
                                   {
                                     'end' => '480',
                                     'start' => '455'
                                   }
                                 ],
          'CLS_S3_Contig2729' => [
                                   {
                                     'end' => '130',
                                     'start' => '119'
                                   },
                                   {
                                     'end' => '220',
                                     'start' => '163'
                                   }
                                 ],
          'CLS_S3_Contig2731' => [
                                   {
                                     'end' => '843',
                                     'start' => '824'
                                   },
                                   {
                                     'end' => '1201',
                                     'start' => '1150'
                                   }
                                 ],
          'CLS_S3_Contig2728' => [
                                   {
                                     'end' => '144',
                                     'start' => '117'
                                   },
                                   {
                                     'end' => '472',
                                     'start' => '437'
                                   }
                                 ],
          'CLS_S3_Contig2721' => [
                                   {
                                     'end' => '168',
                                     'start' => '139'
                                   }
                                 ],
          'CLS_S3_Contig2735' => [
                                   {
                                     'end' => '636',
                                     'start' => '571'
                                   },
                                   {
                                     'end' => '710',
                                     'start' => '677'
                                   },
                                   {
                                     'end' => '810',
                                     'start' => '775'
                                   }
                                 ],
          'CLS_S3_Contig2730' => [
                                   {
                                     'end' => '202',
                                     'start' => '181'
                                   },
                                   {
                                     'end' => '384',
                                     'start' => '361'
                                   }
                                 ]
        };
$VAR2 = {
          'CLS_S3_Contig2721' => [
                                   {
                                     'end' => '169',
                                     'start' => '142'
                                   }
                                 ],
          'CLS_S3_Contig6525' => [
                                   {
                                     'end' => '514',
                                     'start' => '509'
                                   },
                                   {
                                     'end' => '502',
                                     'start' => '493'
                                   },
                                   {
                                     'end' => '508',
                                     'start' => '503'
                                   }
                                 ],
          'CLS_S3_Contig2730' => [
                                   {
                                     'end' => '389',
                                     'start' => '365'
                                   }
                                 ],
          'CLS_S3_Contig4978' => [
                                   {
                                     'end' => '274',
                                     'start' => '271'
                                   },
                                   {
                                     'end' => '388',
                                     'start' => '385'
                                   }
                                 ],
          'CLS_S3_Contig2977' => [
                                   {
                                     'end' => '376',
                                     'start' => '365'
                                   },
                                   {
                                     'end' => '82',
                                     'start' => '77'
                                   },
                                   {
                                     'end' => '90',
                                     'start' => '83'
                                   }
                                 ]
        };
Genename(file1)         start   end     **      Genename(file2)       
+  start   end

CLS_S3_Contig2721       139     168     **      CLS_S3_Contig2721     
+  142     169
CLS_S3_Contig2730       361     384     **      CLS_S3_Contig2730     
+  365     389
[download]

--
seek $her, $from, $everywhere if exists $true{love};

Hi Puundeli,

Thank you very much. It seems that the dumper prints the things perfectly. I tried the code with a larger data set, but still it take into account the unique keys. One way to test the algo is to test file1 against itself. You should print everything out. However, you will see that it prints only one key per gene.

Are we missing anything, here?

thanks,

Pedro