[Bioperl-l] StandAloneBlast parameters

Jason Stajich jason at cgt.duhs.duke.edu
Tue Apr 6 18:04:25 EDT 2004

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

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