[Bioperl-l] StandAloneBlast parameters
lairdm at sfu.ca
Tue Apr 6 18:11:38 EDT 2004
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
> What happens when you do
> 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
SysAdmin/Web Developer, Brinkman Laboratory, MBB Dept.
Simon Fraser University
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