[Bioperl-l] BlastPlus Masker

[Mark A. Jensen]

Hi Nils,
You don't have to specify a mask_data file; the factory should
make it for you; try simply

$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
 -db_name => 'my_masked_db',
 -db_data => 'myseqs.fas',
 -masker => 'dustmasker',
 -create => 1);

-mask_data is there so that pre-made masks can be
applied separately, or so you can name the file that
is produced and preserve it; this is an "advanced feature",
I suppose--
MAJ
----- Original Message ----- 
From: "Nils Müller" <nils.mueller0 at googlemail.com>
To: <bioperl-l at lists.open-bio.org>
Sent: Sunday, March 21, 2010 11:17 AM
Subject: [Bioperl-l] BlastPlus Masker


> Dear all,
>
> I am confused in handeling with maskers in blastplus:
> I have fasta seq. and want to run blast with a low complexity masker like
> dustmasker:
>
> $fac = Bio::Tools::Run::StandAloneBlastPlus->new(
>  -db_name => 'my_masked_db',
>  -db_data => 'myseqs.fas',
>  -masker => 'dustmasker',
>  -mask_data => 'maskseqs.fas',
>  -create => 1);
>
> Is myseqs.fas the same as maskseqs.fas??? I don't want to create a
> maskfile , I only will run blast with a masked file??
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>