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

Matthieu Muffato muffato at ebi.ac.uk
Wed Apr 18 15:42:16 BST 2012

Yes, it will

And the NCTree adaptor only ncRNA trees

On 18/04/12 14:51, Moretti Sébastien wrote:
> Thanks a lot Matthieu, it works now as before now.
> With a ProteinTree adaptor, will fetch_all() return only protein trees ?
>> Hi Sébastien
>> You should call "fetch_all" on the protein tree adaptor. This will give
>> you an array with all the protein trees.
>> Initially, all the protein trees were indeed directly connected to what
>> you call "big_root", but we are now storing there the links between the
>> trees that are part of a bigger structure ("super-tree"), which defines
>> old duplications and distant paralogues.
>> By calling fetch_all_roots() and children(), you go into this internal
>> hierarchy of trees. fetch_all is the preferred way of getting all the
>> "normal" trees in one go.
>> Matthieu
>> On 18/04/12 14:31, Moretti Sébastien wrote:
>>> First, I get a list of all trees:
>>> my $protein_tree_adaptor = $reg->get_adaptor('Multi', 'compara',
>>> 'ProteinTree');
>>> my ($big_root) = @{$protein_tree_adaptor->fetch_all_roots};
>>> my @children = @{$big_root->children()};
>>> then I get a node_id with the node_id() method on each @children
>>> elements.
>>> Now, the 10 trees I have checked had all the "proteinclusterset" tree
>>> type.
>>> What should be the "normal" protein tree type ?

More information about the Dev mailing list