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

Chris Fields cjfields at uiuc.edu
Mon Oct 16 13:21:46 EDT 2006


Bio::Tools::BPlite was placed on the deprecation list a while back (~ rel
1.5); the other related Bio::Tools::BP* modules were also supposed to be on
that list as well.  

If we want to undeprecate (de-deprecate? reprecate?) BPlite we also would
need to do the same for the others.  They must be updated to parse current
BLAST/PSI-BLAST/bl2seq text output, something that Bio::SearchIO::blast is
currently capable of (so the functionality is redundant).  And someone needs
to take them over.

In my opinion it may be more trouble than it's worth as they haven't been
touched in a while.    Seems if we 'revive' BPlite we're not really moving
forward esp. since you have added the PullParser recently and made
substantial improvements to SearchIO.  

Maybe Bio::Index::Blast just needs to be deprecated or rewritten to use
SearchIO?

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


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> Sent: Monday, October 16, 2006 10:44 AM
> To: bioperl-l
> Subject: [Bioperl-l] Should Bio::Tools::BPlite be deprecated?
> 
> I think Chris recently deprecated this, but should it be? For me, its
> POD description justifies its existence, and perhaps more importantly,
> Bio::Index::Blast relies on it.
> 
> I took a quick peek at the latter and it didn't seem trivial to move it
> over to Bio::SearchIO instead.
> 
> Should it be undeprecated?
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