[Bioperl-l] SearchIO and result of StandAloneBlast

[Jason Stajich]

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.

>
> Thanks a lot,
>
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu