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

[Will Spooner]

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
> >
> >
> >
> >
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> >
> 
>