[Bioperl-l] cigar string in GenericHSP

[Jason Stajich]

On Wed, 12 Mar 2003, Marc Logghe wrote:

> Hi Bob,
> >
> > what about the reportwriter methods? am i missing something here?
> No, you're OK.
>
> >
> > on a separate note, it appears from code that I'm writing that using
> > Bio::Tools::Run::StandAloneBlast to run local blast generates
> > GenericHit and GenericHSP objects, not the Blast specific ones. E.g.
> > print $hit->raw_hit_data throws an error. This method is present in
> > Bio::Search::Hit::blast but not Bio::Search::GenericHit. Am I doing
> > something wrong?
> I don't think so. I asked myself the same question a while ago. My
> conclusion was (correct me if I am wrong here) that you end up with a
> Bio::Search::Hit::blast hit object when having run psi blast, the GenericHit
> objects you get after parsing a 'normal' blast.

Steve's stuff (psiblast) will parse "normal" blast as well, soonish
SearchIO::blast will parse PSIBlast along with all the other blast flavors
- but the way StandAloneBlast is implements things it will expect to use
the 'blast' parser for blastall requests.

> Cheers,
> Marc
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu