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

Brian Osborne bosborne11 at verizon.net
Tue Oct 17 03:48:56 UTC 2006


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.

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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