[Bioperl-l] Error when parsing MEME file

Amonida Zadissa amonida at sanger.otago.ac.nz
Wed May 5 05:46:13 EDT 2004

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


#!/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;


Amonida Zadissa
Biochemistry Department
Otago University
Dunedin, New Zealand

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