[ensembl-dev] $protein_tree_adaptor->fetch_all_roots

[Moretti Sébastien]

> Hi Sébastien
>
> There was indeed some work on tags in rel 65, but this should be
> transparent for users.
> However, missing tags are now returning "undef" instead of an empty
> string. Does it match your error ?

I have always tested $tax_level this way:
if ( defined $tax_level && $tax_level ne '' ){ ... }

Currently the script does not go into this if statement.

> That said, every internal node should have a 'taxon_name' tag, and
> leaves shouldn't (same behaviour as in rel 64). Can you give me an
> example of a failing $node_id ?

Here are 2 failing node_id
8   (for ENSGT00470000042273)
248 (for ENSGT00530000064177)


Sébastien

> Cheers,
> Matthieu
>
> On 10/01/12 15:19, Moretti Sébastien wrote:
>> Hi Matthieu,
>>
>> this method works now. Thanks
>>
>>
>> But later in our script things are broken now.
>> my $tree = $protein_tree_adaptor->fetch_node_by_node_id($node_id);
>> my $tax_level = $tree->get_tagvalue('taxon_name');
>>
>> We use this piece of code to parse protein trees and extract specific
>> sub-trees with a chosen taxonomic root.
>>
>> Now, it looks like the taxon_name tag does not exist anymore in tree
>> object.
>>
>> An 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/