[Bioperl-l] Bio::DB::EMBL

[Rodrigo Lopez]

Hi there,

There is another issue to take (or not) into account here: Until sequence
version servers are available it makes little sense to talk about them
(the sequence versions, that is!). The level of operability is restricted
to official releases of EMBL, genbank and ddbj and the corresponding
updates..and in the updates there is only once version unless one cares to
store 'everything' just to keep SV's alive.

Otherwise than this, thanks to Heikki for this effort!

Next: implement Bio::DB:SeqDB which should include all the sequence
databases which conform (or attempt to) the EMBL format. These include:

Swiss-Prot
SPTrEMBL
TrEMBLNew
RemTrEMBL
ENSEMBL + PEP
IMGT/LIGM
IMGTHLA
...
Some of the Patent Databases:
PATENT_DNA
PATENT_PRT
JPO_PRT
(USPO_PRT)



R:)


ps: just teasing Heikki a bit...


On Wed, 4 Apr 2001, Ewan Birney wrote:

> On Wed, 4 Apr 2001, Hilmar Lapp wrote:
> 
> > Jason Stajich wrote:
> > > > >
> > > > > I've just committed Bio::DB::EMBL which has four methods for
> > > > > retrieving entries:
> > > > >
> > > > > get_Seq_by_id()
> > > > > get_Seq_by_acc()
> > > > > get_Seq_by_version()
> > > > > get_Stream_by_batch()
> > > > >
> > > > >
> > > > > Design issues:
> > > > >
> > > > > The get_Seq_by_version() is a new method and should probably be added
> > > > > into
> > > > >
> > 
> > I agree with Ewan's suggestion here. get_Seq_by_acc_version()
> > sounds more intuitive (to me).
> > 
> > As for the interface, I'm not sure. I think if we put it there,
> > implementors should at least be able to fake it if the underlying
> > DB doesn't provide for versioned seqs. E.g., for those
> > get_Seq_by_acc_version() is the same as calling get_Seq_by_acc().
> > Would that make sense?
> 
> We could let implementations throw an exception. This is not a
> particularly nice solution. Hmmmmm. Perhaps it is best to keep it out of
> the interface. 
> 
> 
> I'm undecided now....
> 
> 
> 
>