[Bioperl-l] Taxonomy hierarchy extraction

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


I tried running the below mentioned script and I seem to be getting the following error:
   
  Weak references are not implemented in the version of perl at /usr/lib/perl5/site_perl/5.8.5/Bio/Tree/Node.pm line 76
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.5/Bio/Tree/Node.pm line 76.
Compilation failed in require at my.pl line 7.
BEGIN failed--compilation aborted at my.pl line 7.

  My script looks something like,
   
  #!/usr/bin/perl
  use strict;
#use warnings;
use DBI;
  use Bio::Tree::Node;
use Bio::DB::Taxonomy;
use Bio::DB::Taxonomy::flatfile;
  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;
  
      foreach $field (@extant_children) {
         print "$field";
         print "|";
         print "\n";
      }

  And I am running the script using the command,
   
  perl myscript.pl -v --names names.dmp --nodes nodes.dmp
   
  and I have the nodes.dmp and names.dmp files in the current directory.
   
  Thanks,
  George
  

Jason Stajich <jason at bioperl.org> wrote:
  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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