[Bioperl-l] IO.pm bug?

[Andreas Matern]

Hi,

I do get the same error:

Trailing \ in regex m/^\/ at C:/Perl/site/lib/Bio/Root/IO.pm line 426.

Using win2k, how do I check which version of bioperl I'm running?

# $Id: IO.pm,v 1.21 2002/01/09 16:13:03 jason Exp $

-Andreas



Paul Boutros wrote:
> Hi again,
> 
> Another little glitch I'm having while trying to run StandAloneBlast
> invovles an error from the IO.pm module.
> 
> System: Win2k Pro (sp3)
> Perl: 5.6.1 ActiveState build 631 (all packages are updated)
> BioPerl: 1.00.2
> 
> In short, what is happening is that while looking for the Blast executable
> it tries to strip off the path-separator in a regular expression that is
> causing an error.  The problem is line 426 of IO.pm.  Below is the code
> for the code that is generating the error for me.  Also is a minimal set
> of code that generates the error and that, I believe, is also replicating
> what is going on in IO.pm.
> 
> To be honest, my PERL isn't good enough, and I have *no* clue why this
> gives an error otherwise I would have suggested a fix.  I can just comment
> out the reg-ex for my purposes, so it isn't a big issue for me but I
> wanted to bring it up.
> 
> Minimal Code:
> $PATHSEP = '\\';
> 
> my $exe = 'blastall.exe';
> 
> if ($exe =~ s/^$PATHSEP//) {
> 	print "Error\n";
> 	}
> 
> Actual 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);
> 
> 	}
> 
> # Error Message:
> # Trailing \ in regex m/^\/ at C:/Perl/site/lib/Bio/Root/IO.pm line 426.
> 
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-- 
--------------
Andreas Matern
Bioinformatician
Bioinformatics - Research and Development
Lion Bioscience Research Inc.
141 Portland Street, 10th floor
Cambridge, MA 02139  USA
Phone: 617-245-5483
Fax: 617-245-5499
amatern@lbri.lionbioscience.com
www.lionbioscience.com