[Bioperl-l] StandAloneBlastPlus

Smithies, Russell Russell.Smithies at agresearch.co.nz
Tue Mar 2 14:35:19 EST 2010


If you want to continue using your current version, you could try to delete your old blast db first. 

if($checkbox eq 'yes'){
 unlink "mydb.*"; #or maybe `rm -f mydb.*`
 $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');
}


> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Mark A. Jensen
> Sent: Tuesday, 2 March 2010 4:58 p.m.
> To: Janine Arloth
> Cc: bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] StandAloneBlastPlus
> 
> 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
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
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