[Bioperl-l] StandAlone BLAST on Windows

[Bornman, Daniel M]

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

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