[Bioperl-l] Re: coding custom Gene object
Thu, 23 Aug 2001 15:11:41 -0600 (CST)
I am just about to commit a Transcript class to bioperl-live in
that allows you to have a structured gene class.
The class you want to use is
which uses said Transcript module.
This has methods to get,add,flush:
objects to your transcript. They become those types of features when you
add them, ie $feature might be a SeqFeature::Generic, but when you do
$feature becomes a Promoter.
On Thu, 23 Aug 2001, Gene Cutler wrote:
> I'm looking for some coding guidance for creating some
> Gene/Transcript/Exon objects to allow me to work with my own gene
> database. I am following the ExternalFeature model and have a class
> based on ExternalFeatureFactoryI that pulls out my gene information
> from MySQL. I now need to implement my genes based on
> Bio::SeqFeatureI. However, I'd prefer not to write that from scratch
> but use some of the existing bioperl modules. I'm a little lost on
> where to begin with that. I see three different Gene.pms:
> And, when I took a look at what got returned by
> $contig->get_all_Genes, it was an array of yet another class:
> Gene_Obj.pm. And along with these are various modules for
> transcripts and exons.
> Having stared at the code for all of these modules, they are now
> blurring in my mind. I need a Gene class that implements
> Bio::SeqFeatureI and to which I can add a few custom annotations.
> Would any of the existing Gene classes meet my needs? If not, which
> module(s) should I extend?
NRC Plant Biotechnology Institute
Saskatoon, SK, Canada