[Bioperl-l] SWISS-PROT writing

Hilmar Lapp lapp@gnf.org
Wed, 03 Jan 2001 12:33:32 -0800

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.

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