[Bioperl-l] IO.pm bug?

[Jason Stajich]

okay - can you submit this as a bug report instead.

-jason

On Tue, 20 Aug 2002, 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.
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>

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