[Bioperl-l] StandAloneBlast Bug?

[Jason Stajich]

On Tue, 20 Aug 2002, Paul Boutros wrote:

> 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?
>
Because none of the core developers use windows for their analyses.
You're blazing a new trail here so you're probably going to hit some bugs.

This is to say that we NEED someone to do these things, but you're
probably going to find that you'll find a certain number of bugs on your
own.

Primarily Bioperl has been focused on processing output
from reports not running analyses.   This is starting to change.
StandAloneBlast was written before we had a clear idea of how we wanted to
organize the runnable components so it needs a good going through.

The code is now in the bioperl-run CVS module and it has been reworked
some, but probably not enough to localize all the plaform specific code.

Bug submissions are direct to the server so I'm not sure why it isn't
appearing.



> 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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>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu