[Bioperl-l] SWISS-PROT writing

[Ewan Birney]

On Wed, 3 Jan 2001, Hilmar Lapp wrote:

> Kris Boulez wrote:
> > 
> > >
> > > See above. I'm not sure what we already have in the Bio::Seq::* hierarchy.
> > > If there's no Swiss.pm yet and GenBank/GenPept doesn't fit well, you could
> > > give Bio::Seq::Swiss.pm a start and adopt the parser to instantiate objects
> > > of that class.
> > >
> > The only thing we have now is Bio::Seq::LargeSeq en LargePrimarySeq. Do
> > you plan on having a Bio::Seq::* class for every (complex) sequence type ?
> > 
> 
> Yes, we plan to have a specialized class for every databank, for which the
> attributes its entries carry are not sufficiently reflected in Bio::Seq.pm
> or an already existing class under Bio::Seq::*. This enables us to free the
> basic Seq object from definitions that only pertain to databanks and don't
> make up the essentials of a biological sequence.
> 
> So, molecule(), division() etc will be eventually moved away from
> Bio::Seq.pm. This is even in the task list for 0.7, but with a priority of
> 2, meaning that we want it, but we may decide to skip it this time in order
> to get the release out of the door.

For GenBank/EMBL I have prototype code to check in over here. Looks fine
to me. Swissprot probably needs its own class. 


there is a valid debate about whether swissprot and genbank/embl should
inheriet off a common base class of "rich database sequence objects" (eg,
division is the same) or we should just say that they are different enough
not to stretch this. I hae not done anything on swissprot.


> 
> 	Hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp@gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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