[Bioperl-l] MEME parsing

Stefan Kirov skirov at utk.edu
Tue Feb 11 10:37:45 EST 2003


I have Bioperl-1.0.2 on windows and I was testing the meme parser with 
MEME.3.0.3 output. I get:

-------------------- WARNING ---------------------
MSG: Unrecognized format:
6603                       1311  2.59e-15 GGCGCATTGA 
CAGAAAAATTGAATTCCCACCCCCC AATGAGGAGG

---------------------------------------------------
This is the script
 use Bio::AlignIO;

    $inputfilename = shift;
    $in  = Bio::AlignIO->new(-file => $inputfilename , '-format' => 'meme');


    while ( my $aln = $in->next_aln() ) {
       print "X";
    }
I have tried running meme with and without -print_fasta option (which 
should not matter really, since the parser does not care about this part 
I think, and anyway the error occurs before this part).
Has anyone experienced this? Thanks!
Stefan Kirov



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