[Bioperl-l] Taxonomy hierarchy extraction

Jason Stajich jason at bioperl.org
Sun Jun 17 16:48:05 EDT 2007


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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--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/




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