#!/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