[Bioperl-l] deprecated modules

[Steve Chervitz]

Sounds like a plan to me.  The sooner we reduce Blast parsing to a single
system, the better (preserving functionality, of course :). Some thoughts:

* The scripts in examples/blast should be re-vamped to use the new system.
(This exercise should help assure functional preservation).

* Go through other files containing code that refers to Bio::Tools::Blast
(bptutorial.pl, Makefile.PL, SeqFeature.t) and update them.

* Might be good to have a document we can point people at who wonder how to
migrate their old scripts to the new system and need extra hand-holding.

* For archaeologists or folks who need to refer to older modules that are no
longer in the distribution, you can always access previous releases from
ftp://bio.perl.org/pub/DIST/

Steve

--- Jason Stajich <jason@cgt.mc.duke.edu> wrote:
> Bio::Tools::Blast has been deprecated for a while - I'd like to remove it
> from the trunk.  Additionally I'd like to remove Bio::UnivAln as it too
> has been deprecated.  Steve and I have agreed that
> Bio::SearchIO::psiblast, Bio::Search::HSP::BlastHSP
> Bio::Search::Hit::BlastHit, and Bio::Search::Result::BlastResult will be
> deprecated in 1.2 assuming we get all the functionality moved over to the
> SearchIO::blast and XX::GenericXX objects.
> 
> I can create a DEPRECATED file to list module history like this:
> 
> # These are modules which are deprecated and later removed from the
> toolkit
> 
> Deprecated Modules     Version Deprecated   Version Removed
> --------------------------------------------------------------
> Bio::Tools::Blast            1.0	          1.1
> Bio::Tools::Blast::HSP       1.0		  1.1
> Bio::Tools::Blast::HTML      1.0		  1.1
> Bio::Tools::Blast::Sbjct     1.0		  1.1
> 
> Bio::Tools::WWW		     1.1
> 
> Bio::UnivAln		     1.0		  1.1
> 
> 
> My feeling is that BPlite currently still serves a purpose and should stay
> on the trunk, but it might need some maintence/testing at some point.
> 
> Shout if you don't want to see this happen.
> 
> -jason
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
> 
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=====
Steve Chervitz
sac@bioperl.org

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