[Bioperl-l] Taxonomy hierarchy extraction
Chris Fields
cjfields at uiuc.edu
Mon Jun 18 22:33:40 UTC 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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> ===========================================================
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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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