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

[Brian Osborne]

Daniel,

Yes, it runs on Windows, no problem. Some questions: did you run formatdb?
Can you run blastall from the commandline using these same files?

Brian O.


On 4/21/06 12:49 PM, "Bornman, Daniel M" <bornmand at battelle.org> 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
> 
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