Perl sort genomic positions

Question

I have a list of genomic positions in the format chromosome:start-end

for example

chr1:100-110
chr1:1000-1100
chr1:200-300
chr10:100-200
chr2:100-200
chrX:100-200

I want to sort this by chromosome number and numerical start position to get this:

chr1:100-110
chr1:200-300
chr1:1000-1100
chr2:100-200
chr10:100-200
chrX:100-200

What is a good and efficient way to do this in perl?

Answer 1

Just use the module Sort::Keys::Natural:

use strict;
use warnings;

use Sort::Key::Natural qw(natsort);

print natsort <DATA>;

__DATA__
chr1:100-110
chr1:1000-1100
chr1:200-300
chr10:100-200
chr2:100-200
chrX:100-200
chrY:100-200
chrX:1-100
chr10:100-150

Outputs:

chr1:100-110
chr1:200-300
chr1:1000-1100
chr2:100-200
chr10:100-150
chr10:100-200
chrX:1-100
chrX:100-200
chrY:100-200