[Bioperl-l] StandAloneBlast parameters

[Jason Stajich]

Might be a bug or the module's confusion with the --filter option for
WU-BLAST.

What happens when you do
 $factory->F('F');

-j
On Tue, 6 Apr 2004, Matthew Laird wrote:

> I've been hunting around the docs and google and can't seem to find the
> answer to curiousity I'm having.... I'm trying to set the -F option
> (filter query sequence) for blastall in the
> Bio::Tools::Run::STandAloneBlast module.
>
> In the module code there's a -filter option in %runParams and in the docs
> there's the example:
> @params = ('program' => 'blastn', 'database' => 'ecoli.nt');
> $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
>
> So I try and set 'filter' => 'F' in my code.  Unfortunately this causes
> bioperl to pass -f F to blastall instead of -F F.
>
> Am I just using the wrong parameter to the module or is this a
> capitalization bug?  Thanks.
>
>

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