[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. 
   
  Thanks.
  George

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).


       
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