[ensembl-dev] compara and zebra proteins

[Gregory Jordan]

This would make a *very* good addition to the docs, IMO. In my experience,
undocumented magic strings such as this are a major contributor to many
peoples' fear of the Ensembl APIs!

http://www.ensembl.org/info/docs/Pdoc/ensembl-compara/modules/Bio/EnsEMBL/Compara/DBSQL/MemberAdaptor.html#POD16

On a related note: why is there no $member_adaptor->fetch_by_stable_id()
method? My guess is most 'casual' users have little use for the source
argument anyways, and it's very nonintuitive to have to use the
fetch_by_source_stable_id method with the first argument being undef.

greg

2010/11/25 Andy Yates <ayates at ebi.ac.uk>

> You've spelt the source name incorrectly. Ensembl proteins are known as
> ENSEMBLPEP in compara so your code should look more like:
>
> my $member =
> $member_adaptor->fetch_by_source_stable_id('ENSEMBLPEP','ENSDARP00000030499');
>
> Apart from that your code looks good.
>
> Andy
>
> On 25 Nov 2010, at 10:17, Koray Doğan Kaya wrote:
>
> > Can't I call a zebrafsh protein like this?
> >
> >
> > my $member_adaptor =
> > Bio::EnsEMBL::Registry->get_adaptor('Multi','compara','Member');
> >
> > my $member =
> >
> $member_adaptor->fetch_by_source_stable_id('ENSEMBLPROTEIN','ENSDARP00000030499');
> >
> > # print out some information about the Member
> > print $member->description, "\n";
> >
> > --
> > M.Sc. Koray Dogan Kaya
> > PhD Candidate
> > Bilkent University,
> > Department of Molecular Biology and Genetics
> > 06800 / Ankara
> > Turkey
> > Mobile: (+90) 533 526 09 51
> > Office: (+90)  312 290 24 03
> > e-mail: kkaya at bilkent.edu.tr
> >
> >
> > _______________________________________________
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> > Dev at ensembl.org
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>
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
>
>
>
>
>
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