[Bioperl-l] changes in standaloneblast

[Jason Stajich]

On Mon, 16 Dec 2002, Phillip Lord wrote:

>
>
>
> I've just updated by code base to use the bioperl-run version of
> StandAloneBlast (rather than the version which used to be in
> bioperl-live). It seems to be working differently now, which is
> breaking by code.
>
>
> The blastall function is documented to return....
>
>  Returns :  Reference to a Blast object or BPlite object
>            containing the blast report.
>
>
> My code ....
>
It's in the documentation....

% perldoc Bio::Tools::Run::StandAloneBlast

>  my @params = ('program'  => 'blastp',
>              'database' => 'swissprot',
# Add this:
               '_READMETHOD' => 'BPlite')
>     ;
>
>   my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>   ## set the expectation
>   $factory->e( 100 );
>
>   my @seqs;
>   push @seqs, $seq;
>   return $factory->blastall( @seqs );
>
> used to return a BPLite object at this point
>
>
> (I call $blast_report->nextSbjct ...on the returned object). This now
> fails, because it seems to be returning instead a
>
> Bio::SearchIO::blast
>
> object, which doesn't have the same methods in it.
>
> Can anyone tell me how to get the BPLite object back?
>
> Cheers
>
> Phil
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>

--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu