[Bioperl-l] Bioperl 1.0alpha

[Heikki Lehvaslaiho]

> >   (b) Review by people who should be reviewing.. (!) Doh!
> >
> uh, heh.  Yah.
> Here is the basic gist of what I am concerned about:
> I'm still a little concerned about seqfeatures that should
> be expanded versus the Split Location model.  This is basically when
> someone calls:
> $feat->add_sub_SeqFeature($subfeat,'EXPAND');
> 
> So with the invention of the Bio::Location::Split system for handling
> multiple locations, so I'm not sure we do the right thing for locations
> versus sub features.  Gotta dig some more and come up with appropriate
> tests.
> 
> This also relates to working with locations and when we call trim on a
> sequence and need to renumber the coordinates for the features on the
> subsequence.  Need to develop the tests for this so we can be sure we're
> really acting properly (pretty sure we're not).

I'd like to get refseq/NT/genbank logic into GEnBank.pm, but I can not spare
any time before the hackathon. 

> >
> >
> > Then - branch
> >
> >    - on release, list of modules to prune - I think
> > Bio::Tools::SwissProtParser should go, as it is really waiting for an
> > event based SeqIO framework (now... that is going to be a real shakeup -
> > *definitely* not 1.0 stuff).
> >
> Okay - let's also remove
> Bio::Tools::Fasta (there is no test for this and it is replaced by
>                    Bio::SearchIO)
> 
> Not sure if we want to release with the Biblio objects included?
> Should we remove from a 1.0 branch?

Martin has been working on it. Let's see at the hackathon what is its status
then. If we can have XML parser in there, I can easily add Bio::DB::Medline
and then it might be worth letting it stay.

Aw, I promised to remove the hydrophobicity special meaning from B & Z
characters in Bio::Tools::SeqPattern, I have not done it. I'll doit at the
hackathon unless someone else beats me at it.

	-Heikki
-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
     _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
___ _/_/_/_/_/________________________________________________________