[Bioperl-l] problem parsing MEME file

Stefan Kirov skirov at utk.edu
Tue Sep 21 07:08:06 EDT 2004

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.

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:
>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
>Diego Riano

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