[Bioperl-l] New Bioperl dependency? Sort::Naturally

[Jason Stajich]

Unless necessary I don't know if adding yet another dependency is 
warranted here.

I don't know how complicated the words will be but can't you just strip 
out the numbers and do this in a schwartzian transformation?

#!/usr/bin/perl -w
use strict;
my @arr = qw(single1 contig10 101 contig2 3);
my @sorted = map { $_->[1] } sort { $a->[0] <=> $b->[0] } map { [ 
/(\d+)/, $_] } @arr;
print join("\n", at sorted),"\n";

But I'm not sure how do you want to sort
10 vs contig10 vs singlet10 reliably?

-jason

Florent Angly wrote, On 5/7/10 9:42 PM:
> Hi all,
>
> I am working on updating some of the Bio::Assembly::* modules right now.
> I need to sort a list of IDs. These IDs could be numbers, "words" or a 
> mix of the two, for example:         @arr = ('singlet1', 'contig10', 
> 'contig2',  '101', '3');
>
> I cannot sort them with the numerical sort: sort { $a <=> $b } @array
> This would generates warnings because some of'singlet1' the IDs are 
> numbers.
>
> I cannot sort them lexically: sort @array
> Lexical sorting would not take into account numbers properly and 
> result in:
>     singlet1 contig10 contig2 3 101
>
> So, what I really need is natural sorting, which is not in any core 
> function of Perl. I'd like to use the CPAN module Sort::Naturally for 
> this purpose: nsort @arr
> The results would be what we expect, i.e.:
>     3 101 contig2 contig10 singlet1
>
> Can I add this module as an additional dependency of BioPerl? I 
> imagine that some other modules might want to use this. On the 
> assembly side, it would be used by the writing methods of 
> Bio::Assembly::IO::tigr and ace. Or maybe there is an easy way around 
> my problem that doesn't require any external module?
>
> Florent
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