[Bioperl-l] Bio::*Taxonomy* changes

[Chris Fields]

Wow, we're doing a little bioperl spring cleaning here!  

I agree with Hilmar: create a new module (Bio::Taxon), which claims the
namespace, and deprecate the old ones.

How 'broken', exactly, is Bio::Taxonomy?  The idea behind it seems just
(container for Nodes) but maybe it should just be reconfigured, and all the
classes in directory Bio/Taxonomy deprecated.  Or should we start from
scratch completely?  

Don't know if it has been attempted but it would be nice to have a way for
building taxonomic trees from Node/Taxon information using a Taxonomy-like
container object.  I like the way NCBI does something along these lines with
BLAST output now.

BTW, thanks guys for a rousing discussion!

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Hilmar Lapp
> Sent: Thursday, July 27, 2006 9:29 AM
> To: Sendu Bala
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bio::*Taxonomy* changes
> 
> How do you mean 'process'? You create a new module, and then you
> deprecate the ones you're phasing out. If possible you rewrite the
> implementation to use the new module.
> 
> Not sure this answers your question?
> 
> 	-hilmar
> 
> On Jul 27, 2006, at 10:06 AM, Sendu Bala wrote:
> 
> > Hilmar Lapp wrote:
> >> I don't think the top-level or sub-directory matters at all and I
> >> don't
> >> want anybody to get used to the notion that that may imply anything
> >> (except possibly better thought-out structure for the sub-directory
> >> level). For instance RichSeq is what all rich annotation sequence
> >> format
> >> parsers return, yet it is in a sub-directory.
> >
> > Well, I'm not aware that I've ever used a RichSeq ;). But your
> > point is
> > taken.
> >
> >
> >> I don't any real objection to Bio::Taxon though if that's what you'd
> >> like to name it - although, what will happen to the Bio::Taxonomy
> >> hierarchy then? Phased out?
> >
> > At the moment it seems to me that the Bio::Taxonomy modules (excluding
> > Node) aren't really usable. Jason wrote a comment in t/TaxonTree.t
> > which
> > tests Taxon and Tree:
> >
> > ## I am pretty sure this module is going the way of the dodo bird so
> > ## I am not sure how much work to put into fixing the tests/module
> >
> > FactoryI is strange (it isn't intended to work like any other Bioperl
> > factory) and there are no implementers of it, while Taxonomy.pm itself
> > would be redundant after my Node changes and has implementation
> > issues,
> > though it may make more sense to some people.
> >
> > My vote is phase out.
> >
> >
> > What is the actual process involved in renaming a module in Bioperl?
> > _______________________________________________
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> >
> 
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
> 
> 
> 
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