[Bioperl-l] Error when parsing MEME file

[Stefan Kirov]

Weird.... It worked fine for me, including Amonida's example. Unless it 
is a Windows vs Unix issue, since I wrote and tested the fix under 
Windows. This reminds me of a good movie- "Kill Bill" :-). I should drop 
Win stuff completely I guess.
Thanks Jason!
Stefan

Jason Stajich wrote:

>Something was still wrong with your fix stefan - I committed something
>which should work.  Do a CVS update Amonida and you should have thefix.
>
>As for whether or not Seqio can parse long IDs, it just takes whatever is
>after the > until the 1st space.  We don't try and interpret the ID and
>get accession out of the ncbi id lines by default - although there have
>been proposals on the list for doing this, I can't really remember if
>anyone solved it.  I just end up writing my own id parser if I need a
>particular thing out...  We solve it for the HitI object when parsing
>blast reports and setting accessions.
>
>-jason
>
>On Thu, 6 May 2004, skirov wrote:
>
>  
>
>>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
>>>      
>>>
>>_______________________________________________
>>Bioperl-l mailing list
>>Bioperl-l at portal.open-bio.org
>>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>>
>>    
>>
>
>--
>Jason Stajich
>Duke University
>jason at cgt.mc.duke.edu
>_______________________________________________
>Bioperl-l mailing list
>Bioperl-l at portal.open-bio.org
>http://portal.open-bio.org/mailman/listinfo/bioperl-l
>  
>

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