[Bioperl-l] problem parsing MEME file

[James Thompson]

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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