[Bioperl-l] Parsing Meme

[Tirza Doniger]

I am trying to parse output from meme.

bioperl version: 1.0.2
meme version: 3.0
meme parameters :
meme test.seq  -nostatus -text -minw 30 -maxw 80  -nmotifs 5 -print_fasta > test.out


------------------------
perl program:

#!/usr/bin/perl -w

use Bio::AlignIO;
 
my $alignio = new Bio::AlignIO(-format => 'meme',
			       -file =>'test.out');

while( my $aln = $alignio->next_aln) {
 foreach my $seq ($aln->each_seq) {
	print "\t '", $seq->display_id(), "' \n";
    }   
}
-------------------------------------------

I am receiving the following error message:

-------------------- WARNING ---------------------
MSG: Unrecognized format:
test1      473  1.33e-45 TGGTCTTGAT CTCCTGACCTTGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCCACCGCGCCCGGCCC CAACTATTAT

---------------------------------------------------
If anyone has any idea why this is heppening?

Thanks
Tirza

-- 
Tirza Doniger
Princeton University
Department of Molecular Biology
tdoniger@molbio.Princeton.edu