IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover
some of this, for instance:
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.
On Mar 25, 2013, at 1:40 AM, Carnë Draug wrote:
> 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
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.
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