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

Moretti Sébastien sebastien.moretti at unil.ch
Wed Apr 18 14:51:59 BST 2012

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 ?

Sébastien Moretti
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/

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