[ensembl-dev] protein tree id and tagvalue

Matthieu Muffato muffato at ebi.ac.uk
Wed Jul 4 14:58:45 BST 2012

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).

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)


On 04/07/12 14:45, Moretti Sébastien wrote:
>> Because you call sorted_children() on the root node
> So, what should I use instead of
> my @children = @{$tree->root->sorted_children()}; ?
> $tree->root->children()
> or
> $tree->children()
> do not work at all.

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