[ensembl-dev] protein tree id and tagvalue

Matthieu Muffato muffato at ebi.ac.uk
Wed Jul 4 15:14:19 BST 2012

The initial call to split_tree should use $tree->root, then.

The other solution is to define $tree as 
$tree_adaptor->fetch_by_root_id(487410)->root and you will not need any 
further ->root() call


On 04/07/12 15:10, Moretti Sébastien wrote:
>> children() returns the children of a node in a random order as given by
>> the database, that may vary from one call to another.
>> sorted_children() returns the same children, but in a stable and
>> reproducible order.
>> In your case, you can call any of these two methods, but on $tree (which
>> is at this stage a GeneTreeNode).
> But $tree is not a GeneTreeNode object, it is a GeneTree object in my case:
> my $tree_adaptor = $reg->get_adaptor('Multi', 'compara', 'GeneTree');
> my $tree         = $tree_adaptor->fetch_by_root_id(487410);
> Bio::EnsEMBL::Compara::GeneTree=HASH(0x2a85b40) does not understand
> method Bio::EnsEMBL::Compara::GeneTree::children
> In the documentation I only see root method that returns a GeneTreeNode
> object from a GeneTree object.
>> The code to select subtrees of the appropriate clade should actually be
>> the same as in previous releases. I think only the initial call to get
>> the list of root nodes is different (+ the interpretation of the
>> "Duplication" tag)
>> Matthieu

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