[Bioperl-l] Taxonomy hierarchy extraction

Chris Fields cjfields at uiuc.edu
Mon Jun 18 18:33:40 EDT 2007


As the error implies your local version of perl doesn't seem support  
weak references, which means it doesn't have Scalar::Utils (which was  
added to core after perl 5.6.1, I think).  Try installing  
Scalar::Utils to see what happens.

chris

On Jun 18, 2007, at 5:18 PM, George Heller wrote:

> 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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>   --
>   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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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