[ensembl-dev] protein tree id and tagvalue
Moretti Sébastien
sebastien.moretti at unil.ch
Tue Jul 3 15:14:21 BST 2012
Hi
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',
'ProteinTree');
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 ?
Regards
--
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/
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