[Bioperl-l] Unigene proposal and basic implementation

[Ewan Birney]

On Tue, 16 Apr 2002, Jason Stajich wrote:

> 
> On Tue, 16 Apr 2002, Kris Boulez wrote:
> 
> 
> > We have
> >
> > Bio::AlignIO
> >      AnnSeqIO
> >      MapIO
> >      SearchIO
> >      SeqIO
> >      TreeIO
> >
> > but also
> >
> > Bio::LiveSeq::IO
> >      Variation::IO
> >      Structure::IO
> >      Biblio::IO
> >
> >
> > What do people think about Bio::IO ?
> 
> No - this AlignIO -> LiveSeq::IO transition was designed so we
> don't create 2 top level directories for each new for data system.  But
> it is not part of the unwritten bioperl best practices document.  I'm
> pretty much okay with mixing the two for now but I definitely agree that
> it would be better to use a single paradigm when naming.
> 
> I don't think Bio::IO would be a good way to group though, I really prefer
> that the parser stay closer to the data objects wrt to namespace.

I'm with you Jason. 

  Fine with either Bio::Cluster::IO or
                   Bio::ClusterIO

  Marginal preference for (1).



> 
> Just my opinion though...  Counter arguments welcomed.
> 
> -j
> >
> > Kris,
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> >
> 
> -- 
> Jason Stajich
> Duke University
> jason@cgt.mc.duke.edu
> 
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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