chr1 100 120 feature1
chr1 200 250 feature2
chr2 150 200 feature1
chr2 280 350 feature1
chr3 100 150 feature2
chr3 300 450 feature2

##</code><code>##

chromosome = chr2
start = 160
end = 210

##</code><code>##

#!/usr/bin/perl

use strict;

my %reps = ();
while(my $line = <DATA>){
 $line =~ s/[\n\r]//g;
 my @array = split(/\s+/,$line);
 $reps{$array[0]}{$array[1]}{'end'} = $array[2];
 $reps{$array[0]}{$array[1]}{'rep'} = $array[3];
 }

my $start = 160;
my $end = 210;
my $chr = "chr2";

for my $s (sort {$a<=>$b} keys %{$reps{$chr}}){
 if ($start <= $reps{$chr}{$s}{'end'}) {
  last if $s >= $end;
  print "$chr $s $reps{$chr}{$s}{'end'} $reps{$chr}{$s}{'rep'}\n";
  }
 }

__DATA__
chr1 100 120 feature1
chr1 200 250 feature2
chr2 150 200 feature1
chr2 280 350 feature1
chr3 100 150 feature2
chr3 300 450 feature2