[ensembl-dev] How to update sequences in a compara tree object

[Sébastien Moretti]

Data::Dumper shows something like this:

$tree->{'_parent_link'}->{'_link_node2'}->{'_obj_id_to_link'}->{'Bio::EnsEMBL::Compara::ProteinTree=HASH(0x23bcf88)'}->{'_link_node1'}->...

The 4th key is a reference to another hash.
This key has been stringified and thus it is not easy to guess because 
changes for every run.

I can get alignment information below with a leaf object
     $leaf ( @{$tree->get_all_leaves} )
, update alignment in the leaf object but not in the parent tree object.


A way to do that ?

> Hi
>
> I use compara tree to fetch and edit trees.
> e.g.:
> my $tree = $protein_tree_adaptor->fetch_node_by_node_id('870377');
> ...
>
>
> I can easily remove tree nodes but don't know how to update a sequence
> into the tree object.
> Data::Dumper provides a huge data structure.
> Too huge to be searchable easily.
>
> So, is there a way to update sequence in the tree object without
> changing data in MySQL ?
>
> Thanks

-- 
Sébastien Moretti
Department of Ecology and Evolution,
Biophore, University of Lausanne,
CH-1015 Lausanne, Switzerland
Tel.: +41 (21) 692 4221/4079
http://bioinfo.unil.ch/