[Bioperl-l] Error when parsing MEME file

Stefan Kirov skirov at utk.edu
Wed May 5 13:47:23 EDT 2004

Dear Amonida ,
This is actually a bug. It occurs when you use -revcomp as you have and 
you have a macth on the - strand as you point out. Thanks a lot for 
noticing this bug. I'll commit a bug fix today or tomorrow, so update 
your bioperl (bioperl-live) and let me know if you find any prooblems.

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
>#!/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;
>    }

Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
1060 Commerce Park, Oak Ridge
TN 37830-8026
tel +865 576 5120
fax +865 241 1965
e-mail: skirov at utk.edu
sao at ornl.gov

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