[Bioperl-l] organizing a gene family in memory

[Fields, Christopher J]

IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:

https://metacpan.org/module/Bio::Cluster::FamilyI

My feeling is they were trying to be too inclusive (I think some dbSNP functionality was included here as well, which IMHO may be a bad fit).  Anyway, these haven't changed for many years; you're welcome to take a look at them and see if they fit your needs.

chris

On Mar 25, 2013, at 1:40 AM, Carnë Draug <carandraug+dev at gmail.com> wrote:

> Hi
> 
> I need something to keep a bunch of genes belonging to the same family
> organized. It is more than a plain hash since the family can be
> divided into multiple ways (subfamilies, types and classes) that
> overlap each other, but using a database seems overkill to me. I
> couldn't find a module on CPAN that does it so I might write one if no
> one suggests an alternative. Basically, with it I wanna be able to do
> something like this
> 
>  my $histones = Bio::Family->new(
>      -classes      => ['canonical', 'variant'],
>      -types        => ['H2A', 'H2B', 'H3', 'H4'],
>      -subfamilies => [ ... ],
>  );
> 
>  $histones->add_member ($seqob,
>      -class => 'canonical',
>      -type  => 'H3',
>  );
> 
>  @all_members = $histones->members;
>  @canonicals  = $histones->class('canonical');
> 
> I already wrote a bit of POD for it
> http://bpaste.net/show/UI6GbX5MWmCwGJWerGpq/ and would like some input
> on its design before start coding, as I fear it might be too focused
> for the problem I have at hand. Could someone give me some advice
> about it?
> 
> I'm also thinking that maybe I should write some sort of general perl
> module, outside the Bio::* namespace.
> 
> Thanks,
> Carnë
> 
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