[ensembl-dev] $protein_tree_adaptor->fetch_all_roots

[Matthieu Muffato]

Dear Sébastien,

Thank you for spotting this ! fetch_all_roots indeed broke with some 
database work on the release 65.

I've fixed the code and fetch_all_roots is now working as expected. Can 
you update your CVS checkout ? Otherwise, you can use 
fetch_node_by_node_id(1), which is less generic, but is currently working.

Best,
Matthieu

On 10/01/12 14:40, Moretti Sébastien wrote:
> Hi
>
> We used the following code before and it worked perfectly (at least with
> ensembl 61). Now it does not work anymore with ensembl 65.
>
> my $protein_tree_adaptor = $reg->get_adaptor('Multi', 'compara',
> 'ProteinTree');
> my ($big_root) = @{$protein_tree_adaptor->fetch_all_roots};
> my @children = @{$big_root->children()};
>
>
> Now the children method is undefined:
> Can't call method "children" on an undefined value
>
>
> Could you tell me how to get all gene/protein tree ids from compara now ?
> I guess there is another way to get them.
>
> Thanks
> Regards
>