[Bioperl-l] Error when parsing MEME file

[Stefan Kirov]

Could you please forward me the MEME file you are trying to parse along 
with the motif that fails (if you know it)?
Stefan

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;
>    }
>}
>
>********************************************************************
>
>  
>