[Bioperl-l] Error when parsing MEME file

[skirov]

Amonida,
Wow, you have an amazing amount of ids... I am sure it will be much better if 
you can use a simple ID line like
>X61109
someseq...
Of course I could change the parser... but I am not sure it is worth it.
Jason, forgive my ignorance, but current SeqIO will not parse fasta ID line 
like this one:
>ref|NW_047562.1|Rn1_2084
I guess it will be best if meme parser is in sync with SeqIO with respect to 
IDs.
Stefan

>===== Original Message From Amonida Zadissa <amonida at sanger.otago.ac.nz> 
=====
>Stefan and Jason,
>
>Thanks for your replies. I was using bioperl-1.4 but now I have
>bioperl-live installed. Nevertheless, the problem seems to be there
>but I get new warnings complainging about both strands now.
>
>Argument "-" isn't numeric in addition (+) at
>/opt/share/perl/5.8.3/Bio/LocatableSeq.pm line 167, <GEN0> line 699.
>Argument "+" isn't numeric in addition (+) at
>/opt/share/perl/5.8.3/Bio/Matrix/PSM/InstanceSite.pm line 106, <GEN0>
>line 700.
>
>Could this depend on my installation (which by the way went fine)?
>
>I'm attaching the MEME test file I have used.
>
>Thanks for any help,
>Amonida
>
>On Wed, May 05, 2004 at 02:51:12PM -0400, Stefan Kirov wrote:
>> Fixed now, check it from bioperl-live
>> 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;
>> >   }
>> >}
>> >
>> >********************************************************************
>> >
>> >
>> >
>
>--
>Amonida Zadissa
>Biochemistry Department
>Otago University
>Dunedin, New Zealand