[ensembl-dev] protein tree id and tagvalue

[Moretti Sébastien]

> Hi !
>
> On 03/07/12 16:04, Moretti Sébastien wrote:
>>> Hi Sébastien
>>
>> Hi
>>
>>> The fetch_node_by_node_id(1) trick might not work any more as (1) we are
>>> now storing tree of trees (called "super trees" in Compara), (2) we have
>>> merged the API and the SQL tables of protein and ncRNA trees.
>>>
>>> If you want all the protein trees as they were in the previous release,
>>> please use fetch_all(-tree_type => 'tree', -member_type => 'protein')
>>> from the GeneTreeAdaptor. This will return an arrayref of GeneTree
>>> objects. Each tree has a stable_id and other general properties / tags.
>>> Then, by calling "->root()" on a tree, you will jump to its root node,
>>> on which you can call children() recursively.
>>
>> Do I have also to change the adaptor like this ?
>> my $protein_tree_adaptor = $reg->get_adaptor('Multi', 'compara',
>> 'ProteinTree');
>> becomes
>> my $protein_tree_adaptor = $reg->get_adaptor('Multi', 'compara',
>> 'GeneTree');
>
> Yes, only the GeneTreeAdaptor can return GeneTree objects

I am a bit confused.
What is the best between ProteinTree and GeneTree ?

Am I right saying that ProteinTree has to be associated with fetch_all()
, and GeneTree with fetch_all(-tree_type => 'tree', -member_type => 
'protein') ?


And that an adaptor with ProteinTree will require 
$tree->tree->get_tagvalue('taxon_name')
but an adaptor with GeneTree will require 
$tree->root->get_tagvalue('taxon_name') ???

>>> Regarding the node tags, they have been cleaned up and rationalized.
>>> "Duplication" does not exist any more. Please use "node_type" instead,
>>> which is one of {speciation,duplication,dubious,gene_split} and roughly
>>> maps to Duplication = 0, 2, 1 (respectively). taxon_name still exists
>>>
>>> $protein_tree_adaptor->fetch_all returns all the roots of protein trees
>>> and super-trees. You would still need to update the "Duplication" tag
>>> call and filter out super-trees.
>>
>> So, doing this should work:
>>
>> my $protein_tree_adaptor = $reg->get_adaptor('Multi', 'compara',
>> 'ProteinTree');
>> my @children = @{$protein_tree_adaptor->fetch_all()};
>>
>> for my $tree (@children){
>>      my $node_id  = $tree->root->node_id;
>>      my $taxon    = $tree->root->get_tagvalue('taxon_name')
>> }
>>
>> And $tree->root->get_tagvalue('node_type') to get duplication status.
>
> Not really because the ProteinTree adaptor is used to return root nodes
> (not tree objects). You can directly use "->node_id()" and
> "->get_tagvalue(...)" on $tree
>
>>
>> Does $tree->tree->stable_id(); from API 66 work again ?
>
> Yes, you can call ->tree() on a tree node to jump to the tree object.
>
> To summarize the link between the two objects:
>   - GeneTree::root() returns a GeneTreeNode
>   - GeneTreeNode::tree() returns a GeneTree
>   - GeneTreeNode::children() returns an array-ref of GeneTreeNode
>   - GeneTreeNode::parent() returns a GeneTreeNode
>
> Regards,
> Matthieu

-- 
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/