[Bioperl-l] Re: coding custom Gene object

David Block dblock@gene.pbi.nrc.ca
Thu, 23 Aug 2001 15:55:54 -0600 (CST)

On Thu, 23 Aug 2001, David Block wrote:

> I am just about to commit a Transcript class to bioperl-live in
> Bio/SeqFeature/Gene/Transcript.pm
> that allows you to have a structured gene class.
> The class you want to use is
> bioperl-live/Bio/SeqFeature/Gene/GeneStructure.pm
> which uses said Transcript module.
> This has methods to get,add,flush:
> Promoter
> utr
> Exon
> Intron
> poly_A_site
> 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
> $mygene->add_promoter($feature);
> $feature becomes a Promoter.
> -Dave

I'm in the midst of testing this code.  It seems to work too well.  In the
past, $gene->exons() would return the exons in the order put in to the
gene.  I by default sort them and return them in order.  This breaks some
of the tests.

Should I 
(a) un_default the sort of exons, or 
(b) change the tests, or 
(c) something else?

Lost in Saskatoon,