[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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