[Bioperl-l] SearchIO and result of StandAloneBlast

[Steve Chervitz]

--- Jason Stajich <jason@cgt.mc.duke.edu> wrote:
> On Mon, 25 Mar 2002, Catherine Letondal wrote:
> 
> >
> > Hi,
> >
> > I have tried the 1.0 blast and search modules, and I have some questions:
> >
> > 1) When running a Bio::Tools::Run::StandAloneBlast, I get a
> > Bio::Tools::BPlite object. Is it going to change to a
> > Bio::Search::Result::ResultI compliant object?
> >
> I thought I fixed this - perhaps it still defaults to BPlite but you can
> request a SearchIO object by specifying
> _READMETHOD => "Blast"  (which now uses SearchIO instead of Tools::Blast)
> 
> 
> > 2) When creating a result with the Bio::SearchIO modules from a blast
> > report, I get a Bio::Search::Result::GenericResult, and not a
> > Bio::Search::Result::BlastResult. What is the
> > Bio::Search::Result::BlastResult for then? Only for psiblast?
> 
> Yes, only for psiblast. Steve and I have to figure out how to best merge
> our two solutions to blast parsing. His BlastResult object uses lazy
> parsing, I use GenericResult which is just a simple data structure.
> 
> I'm really not sure how we plan to reconcile this because it really means
> 2 different types of parsers.  I prefer to keep all the parsing methods in
> the SearchIO space but I can understand Steve's desire to push things into
> specialized objects.

The lazy parsing is done only in Bio::Search::HSP::BlastHSP. My aim is to
remove the lazy parsing, most likely into Bio::Factory::BlastHitFactory, where
BlastHSPs are created.

The point of using factories was to permit a SearchIO parser to generate
different types of  Result/Hit/HSP objects depending on what factory is hooked
up to it. This will allow Jason's Generic objects and my Blast objects to
co-exist. Users can plug in the desired factory, including one that they might
write themselves. 

We still need to formalize how SearchIO objects interact with these factories
(e.g., what data is required when telling a factory to create an HSP), so this
factory business is largely at the vision stage.

Steve




=====
Steve Chervitz
sac@bioperl.org

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