[Bioperl-l] GeneStructure & Promoter(s)

Ewan Birney birney@ebi.ac.uk
Mon, 19 Feb 2001 08:11:41 +0000 (GMT)

On Sun, 18 Feb 2001, Hilmar Lapp wrote:

> Thanks for all the comments. So there appears to be some
> controversy about the promoter property of GeneStructure and
> Transcript.
> As of now, TranscriptI has a method promoters() returning an array
> of SeqFeatureI objects. Transcript.pm has also a method
> add_promoter() allowing you to add SeqFeatureI objects.
> One of the key design goals was to create a set of classes that
> can constitute a basis for Ensembl implementations, but are
> generic enough to accomodate other use-cases, too.
> As for the Bioperl 0.7 release, I want the interfaces not to be
> written in stone, but to anticipate possible/necessary changes
> such that actually making them in a future release doesn't break
> backward compatibility.
> In practice this means the following:
> 1) We have to decide now whether to return an array or a scalar in
> promoters(). My point was that Ensembl re-implements anyway, and
> can enforce in the implementation that only a single promoter
> feature be added. Is this okay with everyone?

Who *wants* more than one promoter per transcript? How many yes's are
there? I'm still holding out for one-promoter-per-transcript defined in
the interface if I can get it ;)

(PS - Ensembl does not - currently - have a promoter object. It may well
do in the future and I believe it would have a strict one-to-one
relationship with a Transcript)

> 2) We need to decide now which kind of object to return from
> promoters(): SeqFeatureI, or a newly introduced PromoterI, which
> for the time being can just be a type without added functionality
> (more functionality may be added later on, wouldn't break backward
> compatibility). Or see 3).

I would favour this.

> 3) We better decide now whether to add a property
> regulatory_elements(), returning e.g. a GeneRegulatorI object. BTW
> this could then also be the object returned by promoters(). A
> related question is then also what distinguishes promoters() from
> regulatory_elements().

This is not such a bad idea. I guess regulatory_elements in my view would
be on the gene (not the Transcript). But this is serious "no one really
knows what is going on" terroritory. It would not kill me if we did not do
this at all...

> I've got some time on Monday (tomorrow for me, today for Europe).
> So, please give feedback, I'd really enjoy the GeneStructure
> modules being useful and reasonably stable at the same time.
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                              email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420