[Bioperl-l] Should Bio::Tools::BPlite be deprecated?

Chris Fields cjfields at uiuc.edu
Mon Oct 16 19:03:33 UTC 2006

> Hilmar Lapp wrote:
> > The problem is it is not maintained, and there are outstanding been bug
> > reports.
> >
> > If you un-deprecate it, then we need a response to people who come
> > across problems with it when using it. Either you change the POD to say
> > exactly who and when one should use it (or rather not) and point to the
> > fact that it is unsupported for all other cases.
> >
> > Or what would you suggest?
> I'm not sure.
> Does Bio::Index::Blast even work correctly? Does it suffer from whatever
> bugs Bio::Tools::BPlite has? Is Bio::Index::Blast maintained? Should
> that be deprecated as well?
> Ideally I'd like to see Bio::Index::Blast updated to use Bio::SearchIO
> and then Bio::Tools::BPlite can be deprecated. But like I say, it didn't
> seem trivial (or even appropriate).
> Ultimately I just wanted to solve the warnings in the test suite.
> Thoughts, Chris?

My opinion is we either have to completely support BPlite (and the others)
or drop it altogether.  I don't think we can state "use BPLite only with
Bio::Index::Blast, use SearchIO everywhere else."  That's too inconsistent.

It seems simpler to deprecate the various Bio::Tools::BP* classes and either
fix Bio::Index::Blast to use Bio::SearchIO (which I think Brian is working
on) or deprecate Bio::Index::Blast as well.  

The warnings in the test suite belong to BlastIndex.t, correct?  I updated
using Brian's Bio::Index::blast fix and it passes now w/o warnings.

Christopher Fields
Postdoctoral Researcher - Switzer Lab
Dept. of Biochemistry
University of Illinois Urbana-Champaign

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