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

Moretti Sébastien sebastien.moretti at unil.ch
Wed Apr 18 15:42:57 BST 2012


Perfect.

Thanks

> 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 ?

-- 
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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