[Bioperl-l] Taxonomy hierarchy extraction

Jason Stajich jason at bioperl.org
Mon Jun 18 13:53:28 EDT 2007


It is implemented in the implementing class - DB::Taxonomy is just  
the base class. For example see the flatfile implementation  
Bio::DB::Taxonomy::flatfile

See the scripts/taxa/local_taxonomydb_query.PLS for example using it:
nodes and names are from NCBI taxonomy database.

Here is an un-debugged copy+paste for your question that *should* work.

use Bio::DB::Taxonomy
my $idx_dir = '/tmp';

my ($nodefile,$namesfile) = ('nodes.dmp,'names.dmp');
my $db = new Bio::DB::Taxonomy(-source    => 'flatfile',
                                -nodesfile => $nodesfile,
                                -namesfile => $namesfile,
                                -directory => $idx_dir);
  my $node = $db->get_Taxonomy_Node(-taxonid => '33090');
  my @extant_children = grep { $_->is_Leaf } $node->get_all_Descendents;


-jason

On Jun 18, 2007, at 10:07 AM, George Heller wrote:

> What exactly is the "node n" in the query below. When I issue this  
> query, it says,
>
>   relation "node" does not exist.
>
>   I tried to use the get_all_Descendents method but it looks like  
> in order to do a recursive call it calls the method  
> each_Descendent. This method is not implemented in  
> Bio::DB::Taxonomy. It just has a single line,
>
>   shift->throw_not_implemented();
>
>   Thanks.
>   George.
>
> Hilmar Lapp <hlapp at gmx.net> wrote:
>   I'm a bit confused - it sounds like you have set up a local BioSQL
> database and loaded the NCBI taxonomy into the database. You can now
> use simple SQL to retrieve all descendants of a node in the tree
> given its NCBI taxonID such as
>
> SELECT tn.*, tnm.name FROM taxon tn, taxon_name tnm, node n
> WHERE
> n.ncbi_taxon_id = :taxonID
> AND tn.left_value > n. left_value
> AND tn.right_value < n.right_value
> AND tn.taxon_id = tnm.taxon_id
> AND tn.name_class = 'scientific_name'
>
> BioPerl doesn't have a Taxonomy::biosql module yet (though this would
> seem like a worthwhile thing to add), so you can't use the
> Bio::DB::Taxonomy interface to do this against a BioSQL instance.
>
> However, BioPerl does have support for the flat-file download of the
> NCBI taxonomy database and indexes it, so you can simply use
> Taxonomy::{get_taxon,get_all_Descendants} using the flatfile download
> to achieve what you wanted to do in a less than 5 lines of perl.
>
> Although the recursive implementation of Taxonomy::get_all_Descendants
> () won't be lightning fast, it may still be perfectly fine for your
> application - are you sure it is not?
>
> -hilmar
>
> On Jun 18, 2007, at 12:21 AM, George Heller wrote:
>
>> 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 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 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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> -- 
> ===========================================================
> : Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
> ===========================================================
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