[Bioperl-l] Gene Interfaces in Bioperl 0.7; Review of bioperl 0.7 from Ensembl

Hilmar Lapp hilmarl@yahoo.com
Sat, 17 Feb 2001 14:53:21 -0800

Ewan Birney wrote:
> My only comment is that I would expect
> $transcript->promoter
> to return a single object. A transcript is, in my view, defined to have a
> single promoter (ie, there is one unique starting point in the DNA). Of
> course, this really depends what on earth is "a promoter" --- which we are
> punting on right?

Right. If you're sure your application can only put a single
promoter there, then you can always say ($prom) =
$transcript->promoters() and you won't miss anything.

An option to be able to enforce this as a safety belt could be to
add something like $transcript->is_single_promoter(1), which will
make $transcript->add_promoter($prom) throw an exception if
there's already one added. But that would I think be suitable only
for the implementation, and as I understand it you have your own
implementations in Ensembl anyway, so you can easily enforce that
in your code.

> This model works very well with Ensembl. Once bioperl-0.7 is out and
> stable we should be able to be compatabile  with it very quickly.

Good to hear.

> The only challenge here is implementing aspects of the SeqFeature
> interface on our gene/transcript objects, which prefer to be "location
> -less". This is ok in our new world of rich locations - it is just a
> challenge to implement.

It will be interesting to hear about the experiences you're going
to make there ... :) The only thing missing about the new location
model is really a survival tour in reality.

> Re: Ensembl <-> Bioperl 0.7
> I am pleased to say that with only one addition I was able to get Ensembl
> to pass its entire test suite (390 tests) against Bioperl-live /0.7
> candidate

I'm happy to hear this. :-)

Hilmar Lapp                              email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757