[Bioperl-l] Parsing kegg files

Brian Osborne bosborne11 at verizon.net
Wed Feb 21 12:29:40 EST 2007


Stephen,

I don't know what your eventual goals are but you might want to take a look
at bioperl-network. However, there are problems with this package. One, it
only parses DIP tab-delimited and PSI-MI and it does this last one only
partially (you will get the graph though). Two, it seems to have only a
single developer interested in it, that's me, and few users. In my Bioperl
experience projects like this tend to fade away.

http://www.bioperl.org/wiki/Network_package


Brian O.


On 2/21/07 12:01 PM, "stephen.marshall at novartis.com"
<stephen.marshall at novartis.com> wrote:

> 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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