25 Mar 13:54 2013
Re: organizing a gene family in memory
Fields, Christopher J <cjfields <at> illinois.edu>
2013-03-25 12:54:21 GMT
2013-03-25 12:54:21 GMT
IIRC part of the intent of the cluster modules (Bio::Cluster) was to cover some of this, for instance:. 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', > ); > > <at> all_members = $histones->members; > <at> 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. > > Thanks, > Carnë > > _______________________________________________ > Bioperl-l mailing list > Bioperl-l <at> lists.open-bio.org >