[Bioperl-l] StandAloneBlast parameters

[Matthew Laird]

Actually yes, the other fellow's suggestions of 'F' => 'F' worked fine, 
thanks.  I thought it'd be something like 'filter', guess not. :)  Thanks.

On Tue, 6 Apr 2004, Jason Stajich wrote:

> 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
> 

-- 
Matthew Laird
SysAdmin/Web Developer, Brinkman Laboratory, MBB Dept.
Simon Fraser University