[Bioperl-l] Taxonomy hierarchy extraction

George Heller george.heller at yahoo.com
Sun Jun 17 14:41:55 EDT 2007

Hi all,
  Can anyone point me to some example that uses the get_all_Descendents method from Bio::DB::Taxonomy? I am a newbie at this, and I am not quite sure how to implement it. 

Sendu Bala <bix at sendu.me.uk> wrote:
  George Heller wrote:
> Hi all,
> I am looking at extracting the taxonomy hierarchy for some taxon ids.
> What I plan to do is, for a given taxon id, say 33090, I want to
> extract all taxon ids that are children of this species. I do not
> just want the immediate children, but the children's children and so
> on.
> Any ideas on the way I can go about doing this?

Well, you'll use Bio::DB::Taxonomy presumably, and each_Descendent in
some kind of looping structure. Most easily a recursing sub.

If you happen to code up something neat and efficient, why not share it 
with us and we could add it to the Taxonomy module(s).

Shape Yahoo! in your own image.  Join our Network Research Panel today!

More information about the Bioperl-l mailing list