[Bioperl-l] Taxonomy hierarchy extraction

George Heller george.heller at yahoo.com
Mon Jun 18 00:21:45 EDT 2007


Thanks. And how can I assign the $node here in the below code, such that I can reference it to a particular taxon id record? I want to retrieve all the descendents from the taxonomy hierarchy, given a particular taxon id. 
   
  I have a local db setup, in which I have uploaded data using the load_ncbi_taxonomy.pl script. 
   
  Thanks.
  George
   
  Jason Stajich <jason at bioperl.org> wrote:
    I assume you already figured out how to setup a local taxonomydb?
  

  You just want the extant species/leaves of the tree
  

my @extant_children = grep { $_->is_Leaf } $node->get_all_Descedents;  

  

  -jason
    On Jun 17, 2007, at 11:41 AM, George Heller wrote:

    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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