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

Chris Fields cjfields at uiuc.edu
Tue Oct 17 10:12:09 EDT 2006


> Chris,
> 
> OK. In fact there's no written guarantee that all Bio::Index* modules have
> an id_parser() method. It happens that most do, and it's useful. I'll fix
> the documentation in Bio::Index::Blast and add an enhancement request to
> Bugzilla, may be able to get around to before 1.5.2 release but no
> promises.
> 
> Brian O.

Do the various Bio::Index* modules share a common interface?  

I wouldn't worry too much about it for this release, unless you really have
time.  It is still, after all, a developer's release, and you've noted it in
Bugzilla.  We could try for another dev release in winter (rel 1.5.3, I
guess) to get any bug fixes or new modules added.

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


> On 10/16/06 11:34 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:
> 
> >
> > On Oct 16, 2006, at 10:24 PM, Brian Osborne wrote:
> >
> >> Chris and Sendu,
> >>
> >> Sendu was correct in wondering whether id_parser() in Blast.pm
> >> would work
> >> after the module was altered to use SearchIO but what I've found
> >> out from my
> >> local tests is that id_parser() didn't work when BPlite was being used
> >> either. I can continue to work on this but it's safe to say that
> >> removing
> >> BPlite doesn't cause a problem with id_parser, it was already there.
> >>
> >> Brian O.
> >
> > ....
> >
> > It may be one reason (the main reason?) the method wasn't tested.
> > Maybe it should be removed if it can't be easily fixed; I don't think
> > it makes sense keeping it otherwise.
> >
> > Chris
> >
> > Christopher Fields
> > Postdoctoral Researcher
> > Lab of Dr. Robert Switzer
> > Dept of Biochemistry
> > University of Illinois Urbana-Champaign
> >
> >
> >
> > _______________________________________________
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> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
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