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

[Will Spooner]

Running and parsing in Search are merged in much the same way as 
StandAloneBlast; the SearchIO object is created on the fly, and used when 
the next_result method is called. Search could easily be modified, 
however, to return the SearchIO object itself rather than implementing its 
methods. The advantage of the latter is that the parsed Result tree is 
tied to the user's original Search and its raw results, allowing the whole 
lot to be serialised to a file/database. Is this behaviour (e.g. used for 
offline parsers) likely to be of use to BioPerl developers?

Will

On Thu, 26 Aug 2004, Jason Stajich wrote:

> 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
> > > >
> > > >
> > > >
> > > >
> > > > _______________________________________________
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> > > > Bioperl-l at portal.open-bio.org
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> > > >
> > >
> > >
> >
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> >
> 
> --
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
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