[ensembl-dev] How to get taxonomic level of a gene tree

[Steve Moss]

Dear Julien,

I *think* you can use

my $tax_level = $tree->species_tree_node()->node_name();

or

my $tax_level = $tree->taxonomy_level();

Cheers,

Steve

On 18 December 2014 at 13:42, Julien Roux <julien.roux at unil.ch> wrote:
>
> Dear list,
>
> I used to get the taxonomical level of a gene tree using the following
> command:
> my $tax_level = $tree->get_tagvalue("taxon_name");
> But now I get this message:
> ----------------- DEPRECATED ---------------------
> Deprecated method call in file test.pl line 60.
> Method Bio::EnsEMBL::Compara::GeneTreeNode::get_tagvalue is deprecated.
> The taxon_name tag has been deprecated, support will end with e78. Please
> use species_tree_node() from the gene-tree node to get taxon information
>
> I tried the following command without success:
> my $tax_level = $tree->species_tree_node->get_tagvalue("taxon_id");
> my $tax_level = $tree->species_tree_node->get_tagvalue("taxon_name");
> my $tax_level = ${$tree->species_tree_node}{"taxon_id"};
>
> Any hint how to access this data?
> Thanks a lot
> Julien
>
> --
> Julien Roux
> Marie-Curie postdoctoral fellow
> Department of Ecology and Evolution, University of Lausanne, Switzerland
> http://www.unil.ch/dee/home/menuinst/people/post-docs--
> associates/dr-julien-roux.html
> Tel: +41 78 700 2931
>
>
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-- 

Steve Moss
about.me/gawbul
[image: Steve Moss on about.me]
  <http://about.me/gawbul>
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