[Bioperl-pipeline] Genewise matters(start,stop modification)

[Elia Stupka]

> All I have is the protein id (from similarity_features), with no info
> on the biodatabase it is from.  My idea is to just write a method that
> searches each biodatabase and returns the first sequence with the
> correct accession/display id.
> 
> am I missing something?

Nope that's fine. I really don't mind taking the "risk" of querying
multiple biodatabases at the same time, even though in theory the
namespace is not unique, in practice it is, and we don't want to
complicate matters. If we wanted to complicate matters we would pull out
(a bit crazy) the database name from the blast hit analysis and then we
would have to make sure we use the same nomenclature between analysis in
blast and biodatabase name in bioperl-db.

Much simpler to do what you suggested ;) and the method in biosql is
already written.

Elia

> 
> shawn
> 
> 
> 
> 
> On Tue, 2002-09-10 at 14:00, Elia Stupka wrote:
> > > will take a look. Note sure where to slot it in, prior to storing?
> > 
> > It can be done where you are doing it, just rather than inling the code,
> > put a call to the CoordinateMapper, that's all.
> > 
> > > what other arguments are u thinking about?
> > 
> > Nope that's fine, all I meant is that setup_genewise doesn't say much
> > about the fact that it is setup_genewise_from_blast_hits, if you know what
> > I mean.... no big deal :)
> > 
> > Elia
> > 
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> 
> 

Elia

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