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

Brian Osborne bosborne11 at verizon.net
Mon Oct 16 23:24:59 EDT 2006


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.


On 10/16/06 3:03 PM, "Chris Fields" <cjfields at uiuc.edu> wrote:

>> 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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