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

[Steve Chervitz]

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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