But you can do it with hashes! Just use two hashes, one for each file. Then you can use the keys from data file 1 to find out whether corresponding key exists in the hash from data file 2. Below is a quick example:

#! /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+)/;
    $d_one{$key}{'start'}   = $start;
    $d_one{$key}{'end'}     = $end;
}

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

print "Genename(file1) start  end ** Genename(file2)     start    end\
+n\n";

foreach my $key_one ( keys %d_one ) {
    if( $d_two{$key_one} ) {
        if( $d_two{$key_one}{'start'} >= $d_one{$key_one}{'start'} &&
            $d_two{$key_one}{'start'} <= $d_one{$key_one}{'end'} ) {
                    print "$key_one $d_one{$key_one}{'start'} $d_one{$
+key_one}{'end'}"
                        . "** "
                        . "$key_one $d_two{$key_one}{'start'} $d_two{$
+key_one}{'end'}\n";
                        
            }
    }
}

[download]
Note, the limits are inclusive in my code. It produces the following output: 
cpt2jmo@phantom:~$ ./2_hashes.pl
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]

Update: I removed the readmore -tags, since the code is not that long.

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

In reply to Re: Query through array of array by puudeli
in thread Qurey through array of array by sesemin

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