Dear Brothers,

I have a rather large file (640MB) of coordinates that each show the position (start,end) of a particular feature on a particular chromosome. Something like:

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

[download]

Given another set of coordinates and a chromosome number I want to be able to quickly see if there are any features that the coordinates overlap. For example, given:

chromosome = chr2
start = 160
end = 210

[download]

I'd like the result:

chr2 150 200 feature1

Importantly I need to do a large number of these types of lookups in one go (~1000 or so).

So far I have the following. Now this works and I'm quite happy with the performance but it takes up 1.6GB memory when I read in the full 640MB file which contains over 5 million lines of coordinates.

If it helps and/or you really want to you can get this file from HERE but you'll have to change the column numbers to pull out the right fields!

#!/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

[download]

My questions are:
a) Is there a better way to do this?
b) Can the memory footprint be reduced any?

Many, many thanks for any advice.

Rich

In reply to Reducing memory footprint when doing a lookup of millions of coordinates by richardwfrancis

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