[Bioperl-l] StandAlone BLAST on Windows???

Bornman, Daniel M bornmand at BATTELLE.ORG
Fri Apr 21 14:10:15 EDT 2006


Barry's suggestion has apparently fixed the problem.

My simple script only asked for number of hits which returns "35" and I
am not getting an error msg.

Further testing will say for sure but it looks pretty good.

Thanks Barry!

-Dan 

-----Original Message-----
From: Barry Moore [mailto:barry.moore at genetics.utah.edu] 
Sent: Friday, April 21, 2006 2:01 PM
To: Bornman, Daniel M
Cc: bioperl-l at lists.open-bio.org
Subject: Re: [Bioperl-l] StandAlone BLAST on Windows???

Change

> $ENV{BLASTDIR} = 'C:\\BLASTDB\\data';
to
> $ENV{BLASTDIR} = 'C:\\BLASTDB\\;
or set
>
> $ENV{BLASTDB} = 'C:\\BLASTDB\\data';
and when you do a blastp search don't forget to add
> $ENV{BLASTMAT} = 'C:\\BLASTDB\\data';

BLASTDIR points to your blast executables, and assumes a data directory
underneath that for databases and matrix files.  If you have the
standard setup with the executable in one directory and the databases
and matrix files in a subdirectory 'data'  can set BLASTDIR to take care
of everything.  If you've put that executables, databases, or matrix
files in different locations then you'll want to set BLASTDB to point
directly to the database, and BLASTMAT to the matrix files (probably the
same directory).  I know the ncbi.ini file is supposed to take care of
all of this, but it seems like I had trouble with that approach in the
past, and just went back to setting ENV variables.

Barry

On Apr 21, 2006, at 10:49 AM, Bornman, Daniel M wrote:

> Dear BioPerl Listers,
>
> Does anyone know if the BioPerl StandAloneBlast module works on 
> Windows?
>
> I have a very simple script that will not work correctly.
>
> My PATH is set to 'C:\BLASTDB\bin'
> My database, 'ecoli.nt' is in 'C:\BLASTDB\data' directory
>
> Here is the script:
>
> ## START ##
>
> BEGIN{
> $ENV{BLASTDIR} = 'C:\\BLASTDB\\data';
> }
> use strict;
> use Bio::Seq;
> use Bio::Tools::Run::StandAloneBlast;
>
> my @params = (program  => 'blastn', database => 'ecoli.nt'); my 
> $blast_obj = Bio::Tools::Run::StandAloneBlast->new(@params);
> my $seq_obj = Bio::Seq->new(-id  =>"testquery", -seq 
> =>"TTTAAATATATTTTGAAGTATAGATTATATGTT");
> my $report_obj = $blast_obj->blastall($seq_obj); my $result_obj = 
> $report_obj->next_result; print $result_obj->num_hits;
>
> ## END ##
>
>
> Here is the error message I get:
>
> [NULL_Caption] WARNING: testquery: Unable to open ecoli.nt.nin
>
> ------------- EXCEPTION  -------------
> MSG: blastall call crashed: 256 C:\BLASTDB\bin\blastall.exe -p  blastn

> -d  "\ecoli.nt"  -i  C:\DOCUME~1\Home\LOCALS~1\Temp\QZwYdo9eKx  -o 
> C:\DOCUME~1\Home\LOCALS~1\Temp\ADP2OcZw8z
>
> STACK Bio::Tools::Run::StandAloneBlast::_runblast
> C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:732
> STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
> C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:680
> STACK Bio::Tools::Run::StandAloneBlast::blastall
> C:/Perl/site/lib/Bio/Tools/Run/StandAloneBlast.pm:536
> STACK toplevel localblast.pl:12
>
> --------------------------------------
>
>
> Thank You,
>
> Daniel Bornman
> Researcher
> Battelle Memorial Institute
> 505 King Ave
> Columbus, OH 43201
> 614.424.3229
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l




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