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

[Shawn]

> 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.

the alternative is to get the db_file name from the analysis object,
read the sequence directly from the flat file we blast against
using Bio::DB::Fasta. but of course, using a db is preferred but since
the flat file exist anyways.....

small issue.
I will got ahead and do it thru biosql, 

shawn


> 
> 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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