[Bioperl-l] StandAloneBlast Bug?

[Paul Boutros]

Hi once again,

After commenting out the troublesome reg-ex in IO.pm I now get an error in
StandAloneBlast.pm

Basically, it is submitting my parameter list to the command-line without
the executable name concatenated in the front.  Looking at the source
code, it appears that:
$executable = 'blastall'
but
$PROGRAMS{$executable} = '';

Again, I can get around this by just using:
my $commandstring = $executable . $param_string;

but I am curious why I am getting so many little bugs.  Is there something
wrong with my installation?

The source code that generates this and the error messages are below.

Code:
### INCLUDES
use strict;
use Bio::Tools::Run::StandAloneBlast;
use Bio::SeqIO;

### LOCALS
my @params = (
		'program'	=> 'blastn',
		'database'	=> 'est_others'
		);

### OBJECTS
my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);

my $seqfile = Bio::SeqIO->new(
		-file		=> 'test2.fasta',
                -format		=> 'fasta'
		);


### PROCESSING

while (my $input = $seqfile->next_seq() ) {

	$factory->blastall($input);

	}


Errors (note that I edited StandAloneBlast.pm to track down the error
location, so the line-number might be off by two or three):

C:\DOCUME~1\Paul\dev\bioperl>perl -w test_local_blast.pl
'-p' is not recognized as an internal or external command,
operable program or batch file.

------------- EXCEPTION  -------------
MSG: blastall call crashed: 256  -p  blastn  -d
C:\docume~1\paul\blast\data\est
_others  -i  C:\temp\F2qCfGyWwn  -o  C:\temp\8AOfaWSQfY

STACK Bio::Tools::Run::StandAloneBlast::_runblast
C:/Perl/site/lib/Bio/Tools/Run
/StandAloneBlast.pm:605
STACK Bio::Tools::Run::StandAloneBlast::_generic_local_blast
C:/Perl/site/lib/Bi
o/Tools/Run/StandAloneBlast.pm:567
STACK Bio::Tools::Run::StandAloneBlast::blastall
C:/Perl/site/lib/Bio/Tools/Run/
StandAloneBlast.pm:456
STACK toplevel test_local_blast.pl:27

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