[Bioperl-l] Parsing kegg files
stephen.marshall at novartis.com
stephen.marshall at novartis.com
Wed Feb 21 17:01:00 UTC 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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