[Bioperl-l] Bio::Tools::Run::Search proposal

[Jason Stajich]

hmm - SearchIO should be for parsers only - have you merged running and
parsing in the same module? Bio::Tools::Run::Search is a fine place in
terms of namespace but as steve said they could could live in the
bioperl-live CVS module.

-jason
On Thu, 26 Aug 2004, Will Spooner wrote:

> Thanks Steve,
>
> As the module ISA Bio::SearchIO at the moment, could
> Bio::SearchIO::Runnable be the right class?
>
> No tests yet ;)
> I will implement something, but the problem is, of course, dependency on
> 3rd party binaries.
>
> I'll mail the code to you off-list.
>
> Will
>
> On Wed, 25 Aug 2004, Steve Chervitz wrote:
>
> > Will,
> >
> > Sounds good to me. I'd be happy to sponsor you. Couple of things:
> >
> > 1) As for where to put it, seems reasonable to put in under
> > bioperl-live rather than bioperl-run, since the StandAlone/RemoteBlast
> > modules would be re-tooled to use it.
> >
> > 2) Have you written tests for it?
> >
> > Steve
> > --
> > Steve Chervitz
> > sac at bioperl d0t org
> >
> > On Aug 25, 2004, at 1:36 AM, Will Spooner wrote:
> >
> > > I have a proposal for a new BioPerl component which provides a common
> > > programatic interface to tools used for searching sequence databases
> > > (wublast, ncbiblast, blat, ssaha etc). It lives in the
> > > Bio::Tools::Run::Search namespace, but this could easily be changed if
> > > appropriate. Also, the code already exists, and is being used in anger
> > > (which is nice).
> > >
> > > Functionality is similar to StandAloneBlast, which could easily be
> > > modified to interface this new system.
> > >
> > > If this is of interest, and someone would like to 'sponsor' its
> > > inclusion
> > > into BioPerl, please let me know.
> > >
> > > Here's some detail;
> > >
> > > NAME
> > >        Bio::Tools::Run::Search - Driver for running Sequence
> > >        Database Searches
> > >
> > > SYNOPSIS
> > >        use Bio::Tools::Run::Search;
> > >        # Create a new search object
> > >        my $search = new Bio::Tools::Run::Search(-method=>'wublast');
> > >
> > >        # Initialise search
> > >        $search->database( '/path/to/my_cdna.fa' ); #method-specific
> > >        $search->seq( $seq );  #Bio::SeqI object
> > >        $search->option( 'E','1' );
> > >
> > >        # Run search
> > >        print "Command: ". $search->command . "\n";
> > >        $search->run;
> > >        while( $search->running ){ wait( 10 ) }
> > >        if( $search->error ){ die( $search->error );
> > >
> > >        # Get results
> > >        print "Report: " . $runnable->report; # Method-specific report
> > >        while( my $res = $runnable->next_result ){ # ResultI object
> > >          foreach my $hsp( map{$_->hits} $res->hits ){ # HSPI object
> > >            # Do stuff
> > >          }
> > >        }
> > >
> > >
> > > DESCRIPTION
> > >        A driver for running Sequence Database Searches (blast,
> > >        ssaha etc). This object serves as a wrapper for the meth-
> > >        ods in Bio::Tools::Run::Search::*, (similar approach SeqIO
> > >        and SearchIO).
> > >
> > >        Search results are available as
> > >        Bio::Search::Result::ResultI objects, or as raw output
> > >        produced by the search method.
> > >
> > > ----
> > >
> > > Regards,
> > >
> > > Will
> > > ---
> > > William Spooner
> > > whs at ebi.ac.uk
> > >
> > >
> > >
> > >
> > > _______________________________________________
> > > Bioperl-l mailing list
> > > Bioperl-l at portal.open-bio.org
> > > http://portal.open-bio.org/mailman/listinfo/bioperl-l
> > >
> >
> >
>
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--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu