[ensembl-dev] GeneTree deprecated tag

[Sébastien Moretti]

Hi

found solution at
http://lists.ensembl.org/pipermail/dev/2014-December/010674.html

Next time I will search there before ;-)
The worst being that it was asked by a colleague next door.

 > Hi
>
> I used to use
>     $taxon_level = $tree->get_value_for_tag('taxon_name');
> with $tree as GeneTree adaptor.
>
> With Ensembl API 79, it looks get_value_for_tag (or get_tagvalue) method
> is deprecated
> And "taxon_name" tag is also deprecated.
>
> It is now recommended to use species_tree_node method but it does not
> work with "taxon_name" tag.
> ERR: Can't call method "left_index" on an undefined value
>
>
> So what is the proper way to get it now?
>
>
> CODE:
> my $reg = 'Bio::EnsEMBL::Registry';
> $reg->load_registry_from_db(
>              ...
> );
> my $tree_adaptor       = $reg->get_adaptor('Multi', 'compara', 'GeneTree');
> my $ncbi_taxon_adaptor = $reg->get_adaptor('Multi', 'compara',
> 'NCBITaxon');
>
> my $tree    = $tree_adaptor->fetch_by_root_id(375021); # id example
> my $tax_level = $tree->species_tree_node('taxon_name');
> my $deepest_node_tax = $ncbi_taxon_adaptor->fetch_node_by_name($tax_level);
> my $left_tax         = $deepest_node_tax->left_index;
>
> Regards

-- 
Sébastien Moretti
Staff Scientist
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://selectome.unil.ch/ http://bgee.unil.ch/