[Bioperl-l] Taxonomy hierarchy extraction

Hilmar Lapp hlapp at gmx.net
Mon Jun 18 18:50:38 EDT 2007


The perl version appears to be 5.8.5 though, so something strange  
appears to be going on too.

George, can you please post the output of

	$ /usr/bin/perl -V

-hilmar

On Jun 18, 2007, at 6:33 PM, Chris Fields wrote:

> 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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>>     --
>>   Jason Stajich
>>   jason at bioperl.org
>>   http://jason.open-bio.org/
>>
>>
>>
>>
>>
>>
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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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-- 
===========================================================
: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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