[Bioperl-l] Error when parsing MEME file

[Jason Stajich]

can you also send an example MEME report which can be used to reproduce
the problem.

-j
On Wed, 5 May 2004, Amonida Zadissa wrote:

> Hi everyone,
>
> I'm trying to parse a MEME file using the Bio::Matrix::PSM
> modules but I'm experiencing problems and was hoping someone on
> the list could help me.
>
> The script is attached below. I get a warning saying the
> following for each "problematic" instance:
>
> Argument "-" isn't numeric in addition (+) at /opt/share/perl/5.8.3/Bio/Matrix/PSM/InstanceSite.pm line 106, <GEN0> line 1164.
>
> Whenever the strand sign is negative the start position is
> assigned the sign and the score is assigned the start position,
> so everything seems to shift one column. This happens only
> if the strand is negative. Note that '$instance' becomes a
> Bio::Matrix::PSM::InstanceSite object.
>
> Is this a parsing error in "InstanceSite.pm" or is my script
> somehow wrong?
>
> Would appreciate any help and by the way thanks for providing this
> forum!
>
> Cheers,
> Amonida
>
> ********************************************************************
> #!/usr/bin/perl -w
>
> use strict;
> use warnings;
> use Bio::Matrix::PSM::IO;
>
> my $psmIO = new Bio::Matrix::PSM::IO(	-file   => 'meme.file',
> 					-format => 'meme');
>
> while (my $psm = $psmIO -> next_psm) {
>     my $instances = $psm -> instances;
>     foreach my $instance (@{ $instances }) {
>     my $start = $instance -> start;
>     my $score = $instance -> score;
>     }
> }
>
> ********************************************************************
>
>

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