[ensembl-dev] How to get a tree stable id ?

[Matthieu Muffato]

Hi Sébastien

We have updated the class hierarchy for gene trees in e66, and will 
finish to do so in e67

The new way of getting the tree stable_id from a node (e.g. the return 
value of fetch_node_by_node_id) is $node->tree->stable_id

->tree() returns a GeneTree object which contains the tree-wide values, 
leaving in the nodes the node-specific attributes.

Matthieu

On 18/04/12 11:23, Moretti Sébastien wrote:
> Hi
>
> with the ensembl 66 API, I cannot get the gene tree stable id I used to
> get before with previous ensembl API.
>
> I build a protein tree adaptor, fetch a node with a node_id but cannot
> get the ENSGT00* id anymore.
>
>
> e.g. with node_id = 2
>
> my $tree = $protein_tree_adaptor->fetch_node_by_node_id($node_id);
> my $stable_id = $tree->node_id;
>
> This returns 2, and not the ENSGT00* id I expect.
> I cannot see any ENSGT00* strings with Data:Dumper in the $tree object.
>