[Bioperl-l] problem parsing MEME file

[Stefan Kirov]

James,
Seems great to me so far. Jason, I think it is reasonable to create an 
account for James. I am not sure who is handling this, can you help? I 
know the e-mail, but I don't know the person.
Stefan

James Thompson wrote:

>Stefan,
>
>  
>
>>>That does make sense, I'll get started on it this weekend. I think I'll try
>>>my hand at adding Bio::Matrix::PSM::ProtMatrix, a lot of the DNA stuff seems
>>>hardcoded into the SiteMatrix object.
>>>      
>>>
>
>  
>
>>Indeed, it is my fault, but you know everyone does what he is really 
>>interested in....
>>    
>>
>
>That makes sense. There's a lot of clever stuff in SiteMatrix.pm, so this might
>take me a bit of time to generalize to amino acid alphabets.
>Bio::Matrix::PSM::ProtMatrix is under development as we speak, should I talk to
>Chris about getting CVS access to upload what I've done thus far? Right now
>I've got the constructor and should I talk to Chris about getting CVS access to
>upload what I've done thus far? Right now I've got the constructor finished and
>tested, and I'll probably ask for input on how to finish out a few of the
>methods (especially calculating the IUPAC consensus for amino acids and
>returning regular expressions for matrices). 
>
>You can view what I've done so far here:
>
>http://bioinformatics.rit.edu/~tex/bioperl/
>
>I've basically ripped off SiteMatrix.pm and I'm translating it subroutine by
>subroutine. I'll keep you and the list posted as I keep working on this. :)
>
>James Thompson
>
>On Tue, 21 Sep 2004, Stefan Kirov wrote:
>
>  
>
>>I had a similar problem in the past and never got an answer from the guy 
>>who wrote the parser. There is also Bio::Matrix::PSM::IO::meme, but it 
>>works only on DNA.
>>James Thompson  has offered to write a psi-blast parser and will create 
>>objects that will also be useful for a protein meme parser. Then it will 
>>be easy to add this functionality to Bio::Matrix::PSM::IO::meme.
>>Stefan
>>
>>Diego Riano wrote:
>>
>>    
>>
>>>Hi all
>>>
>>>I have written a small script to parse MEME results, but I am getting
>>>and error.  I am using Bioperl 1.4 and MEME 3.0.10, it should work but
>>>if does not.  could anyone help me?
>>>
>>>Here is the script:
>>>
>>>#!/usr/bin/perl
>>>
>>>use strict;
>>>use warnings;
>>>
>>>use Bio::AlignIO;
>>>
>>>my $inputf = "$ARGV[0]";
>>>my $in  = Bio::AlignIO->new(-file => $inputf,
>>>                           -format => 'meme');
>>>
>>>
>>>while ( my $aln = $in->next_aln() ) {
>>>       print "X\n";
>>>   }
>>>
>>>This is the error i got:
>>>
>>>-------------------- WARNING ---------------------
>>>MSG: Unrecognized format:
>>>6_04024                     163 5.87e-128 DYSCGGDDSG
>>>TEEEQAAFMKELERFYREKLMEFKPPKFYGEGLNCLKLWRQVTGLGGYDQVTSCKLWRQVGESFKPPKTCTTVSWTFRNFYEKALLEYEKHKIETGEFQV AASNLTERIT
>>>
>>>---------------------------------------------------
>>>
>>>thanks
>>>
>>>Diego Riano
>>> 
>>>
>>>      
>>>
>>_______________________________________________
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>>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