[Bioperl-l] Unigene proposal and basic implementation

[Ewan Birney]

On Mon, 15 Apr 2002 andrew@anatomy.otago.ac.nz wrote:

> Ewan Birney wrote:
> 
> >In your modules listed above do they
> >
> >   (a) go into the Bio:: namespace (Bio::Unigene etc?)
> 
> Yes.
> 
> >   (b) inheriet from Bio::Root::Root.pm?
> 
> Yes.
> 
> >   (c) use Bioperl conventions of new functions looking like
> >
> >       $uni_io = Bio::UnigeneIO->new( -file => 'somefile');
> 
> Yes.

Ok. I think time for a cvs account and you can get to check them in. 


Could you describe (before you check them in) a little more detail - terse
is fine, for example


  Bio::Unigene
 
 methods
      gene_id
      ungene_id
      etc


and

  Bio::UnigeneIO
      next_unigene

or whatever.


BTW - thinking about it, I suspect that we should have the following
abstraction/namespace


   Bio::Seq::ClusterI
      : methods attached to ClusterI which mainly have
      ->seq_ids(); # primary accession of sequences clustered

      ->annotation(); # Bio::Annotation::Collection associated with the
cluster


and I think the name space for unigene is probably best not top level but
instead


   Bio::Seq::Unigene; # inheriets from Bio::Seq::ClusterI

   Bio::Seq::UnigeneIO;



Any other thoughts? Andrew - we should kick this around on the list for 2
or 3 days before you check stuff in. Remember - whoever codes it wins the
argument, so you are in a strong position ;)



    

> 
> Cheers, Andrew.
> 
> 

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