[Bioperl-l] StandAloneBlast parameters

Matthew Laird biolist at brinkman.mbb.sfu.ca
Tue Apr 6 17:38:10 EDT 2004

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.

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

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