[ensembl-dev] protein tree id and tagvalue

Moretti Sébastien sebastien.moretti at unil.ch
Tue Jul 3 15:14:21 BST 2012


It looks the compara API has again a bit changed between releases 66 and 67.
I have a script running on ensembl 64 but don't know how to make it 
compatible with ensembl 67 (API 66 code style does not work).

Here is a sample of my script:

my $protein_tree_adaptor = $reg->get_adaptor('Multi', 'compara', 
my $root = $protein_tree_adaptor->fetch_node_by_node_id(1);

my @children = @{$root->children()};
for my $tree (@children){
     print $tree->node_id;
     print $tree->get_tagvalue('Duplication');
     print $tree->get_tagvalue('taxon_name');

$tree->get_tagvalue('Duplication') and $tree->get_tagvalue('taxon_name') 
are undefined.

Using my @children = @{$protein_tree_adaptor->fetch_all}; gives less 
undefined variables but yet not what's expected.

Any idea ?

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/

More information about the Dev mailing list