This might help you get started. 
#!/usr/bin/perl

use strict;

my $file_1 = <<END;
chr1    3204562    3661779
chr1    4334223    4350673
chr1    4481008    4486694
chr1    4764014    4775968
chr1    4797773    4836816
chr1    4847574    4887987
chr1    4847574    4887987
chr1    4848208    4887987
chr1    4900049    5009660
chr1    5073053    5152630
END

my @boundary_records;
open( my $file, '<', \$file_1 )
  or die( "Error could not open $file_1" );
  while( <$file> ) {
      push( @boundary_records, [ split( /\s+/ ) ] );
  }
close( $file );

my $count = 0;
while( <DATA> ) {
    chomp;
    my @test_records = split( /\s+/ );
    for my $i (@boundary_records) {
        if ( $test_records[1] eq $i->[0]
          and $test_records[2] >  $i->[1]
          and $test_records[3] <  $i->[2] ) {
            $count++;
        }
    }

    print "$_ = $count\n";
    $count = 0;
}

__DATA__
Xkr4    chr1    3204562    3661779    -    3    457.217
Rp1    chr1    4334223    4350673    -    4    16.45
Sox17    chr1    4481008    4486694    -    5    5.686
Mrpl15    chr1    4764014    4775968    -    5    11.954
Lypla1    chr1    4797773    4836816    +    9    39.043
Tcea1    chr1    4847574    4887987    +    10    40.413
Tcea1    chr1    4848208    4887987    +    10    39.779
Rgs20    chr1    4900049    5009660    -    5    109.611

[download]

In reply to Re: Searching and Coutning using 2 files with multiple columns by bichonfrise74
in thread Searching and Coutning using 2 files with multiple columns by shart3

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
to format your post, it's "PerlMonks-approved HTML":


  • Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!
  • Titles consisting of a single word are discouraged, and in most cases are disallowed outright.
  • Read Where should I post X? if you're not absolutely sure you're posting in the right place.
  • Please read these before you post! —
  • Posts may use any of the Perl Monks Approved HTML tags:
    a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr
  • You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)
            For:     Use:
    & &amp;
    < &lt;
    > &gt;
    [ &#91;
    ] &#93;
  • Link using PerlMonks shortcuts! What shortcuts can I use for linking?
  • See Writeup Formatting Tips and other pages linked from there for more info.