[Bioperl-l] Parsing kegg files

stephen.marshall at novartis.com stephen.marshall at novartis.com
Wed Feb 21 12:01:00 EST 2007


Hello
I"m trying to parse a Kegg file and I can't seem to get at the pathway 
information... Here's a snippet of my code. I only see dblink and 
description as annotation

use Bio::SeqIO;

my $stream = Bio::SeqIO->new(-file => $filename, -format => 'KEGG');

while ( my $seq = $stream->next_seq() ) {
        # do something with $seq
        my $id = $seq->display_id();
        print "$id:";
        my $ann = $seq->annotation();
        foreach my $key ( $ann->get_all_annotation_keys() ) {
                my @values = $ann->get_Annotations($key);
                foreach my $value ( @values ) {
                        print "Annotation: ",$key," value: 
",$value->as_text,"\n";
                }
        }

}
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