Perl sort genomic positions - perl

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

Answer 2

You can sort this by providing a custom comparator. It appears that you want a two level value as the sorting key, so your custom comparator would derive the key for a row and then compare that:
# You want karyotypical sorting on the first element,
# so set up this hash with an appropriate normalized value
# per available input:
my %karyotypical_sort = (
1 => 1,
...
X => 100,
);
sub row_to_sortable {
my $row = shift;
$row =~ /chr(.+):(\d+)-/; # assuming match here! Be careful
return [$karyotypical_sort{$1}, $2];
}
sub sortable_compare {
my ($one, $two) = #_;
return $one->[0] <=> $two->[0] || $one->[1] <=> $two->[1];
# If first comparison returns 0 then try the second
}
#lines = ...
print join "\n", sort {
sortable_compare(row_to_sortable($a), row_to_sortable($b))
} #lines;
Since the calculation would be slightly onerous (string manipulation is not free) and since you are probably dealing with a lot of data (genomes!) it is likely you will notice improved performance if you perform a Schwartzian Transform. This is performed by precalculating the sort key for the row and then sorting using that and finally removing the additional data:
#st_lines = map { [ row_to_sortable($_), $_ ] } #lines;
#sorted_st_lines = sort { sortable_compare($a->[0], $b->[0]) } #st_lines;
#sorted_lines = map { $_->[1] } #sorted_st_lines;
Or combined:
print join "\n",
map { $_->[1] }
sort { sortable_compare($a->[0], $b->[0]) }
map { [ row_to_sortable($_), $_ ] } #lines;

Answer 3

It looks to me like you want to sort in order of the following:
By Chromosome Number
Then by the Start Position
Then (maybe) by the End Position.
So, perhaps a custom sort like this:
use strict;
use warnings;
print sort {
my #a = split /chr|:|-/, $a;
my #b = split /chr|:|-/, $b;
"$a[1]$b[1]" !~ /\D/ ? $a[1] <=> $b[1] : $a[1] cmp $b[1]
or $a[2] <=> $b[2]
or $a[3] <=> $b[3]
} <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

Answer 4

You could do something like this the following script, which takes a text file given your above input. The sorting on the chromosome number would need to change a bit because it's not purely lexical or numerical. But i'm sure you could tweak what I have below:
use strict;
my %chromosomes;
while(<>){
if ($_ =~ /^chr(\w+):(\d+)-\d+$/)
{
my $chr_num = $1;
my $chr_start = $2;
$chromosomes{$1}{$2} = $_;
}
}
my #chr_nums = sort(keys(%chromosomes));
foreach my $chr_num (#chr_nums) {
my #chr_starts = sort { $a <=> $b }(keys(%{$chromosomes{$chr_num}}));
foreach my $chr_start (#chr_starts) {
print "$chromosomes{$chr_num}{$chr_start}";
}
}
1;

Answer 5

There is a similar question asked and answered here:
How to do alpha numeric sort perl?
What you are likely looking for is a general numeric sort, like using sort -g.