[ensembl-dev] GeneTree deprecated tag

[Matthieu Muffato]

Hi Sébastien,

Yes, the taxonomy annotation can now be fetched this way:
$gene_tree_node->species_tree_node();  [returns a SpeciesTreeNode object]
$gene_tree_node->species_tree_node()->node_name;
$gene_tree_node->species_tree_node()->taxon_id;
$gene_tree_node->species_tree_node()->taxon;    [returns a NCBITaxon object]
$gene_tree_node->species_tree_node()->taxon->left_index;

Matthieu

On 30/03/15 16:20, Sébastien Moretti wrote:
> 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
>

-- 
Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-145
Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468