[Bioperl-l] StandAloneBlastPlus

Mark A. Jensen jensen at fortinbras.us
Mon Mar 1 22:58:09 EST 2010


Hi Janine--
You'll need to get the latest version of Bio/Tools/Run/StandAloneBlastPlus.pm 
(rev. 16878).
Then the -overwrite parameter will actually work, and you can write

if($checkbox eq 'yes'){


$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-prog_dir => "/usr/local/ncbi/blast/bin",
-db_name  => 'mydb',
-db_data  => 'xxx.fa',
-overwrite   => 1);
}
else{

$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
   -db_name => 'mydb');
}

MAJ

----- Original Message ----- 
From: "Janine Arloth" <janine.arloth at googlemail.com>
To: <jensen at fortinbras.us>
Cc: <bioperl-l at lists.open-bio.org>
Sent: Monday, March 01, 2010 11:25 AM
Subject: StandAloneBlastPlus


Hello,

I am running blast+ and want to create blastdb, depending on a checkbox. That 
means when mydb is to old then I want to rebuilt the blastdb files and create a 
''new'' db.
When the latest versions of my files is ok, then  blast should ran with the 
existing db.
Using this code, there I  will never built a new db. It is creating and than it 
does not create a new one.


if($checkbox eq 'yes'){


$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
-prog_dir => "/usr/local/ncbi/blast/bin",
-db_name  => 'mydb',
-db_data  => 'xxx.fa',
-create   => 1);
}
else{

$fac = Bio::Tools::Run::StandAloneBlastPlus->new(
   -db_name => 'mydb');
}

Thanks for helping



More information about the Bioperl-l mailing list