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

Julien Roux julien.roux at unil.ch
Thu Dec 18 13:42:11 GMT 2014

Dear list,

I used to get the taxonomical level of a gene tree using the following 
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 

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 Roux
Marie-Curie postdoctoral fellow
Department of Ecology and Evolution, University of Lausanne, Switzerland
Tel: +41 78 700 2931

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