[ensembl-dev] find_leaf_by_name in ensembl Metazoa

[Matthieu Muffato]

Hi Sébastien

This happens because the names of the gene tree leaves are protein IDs 
and ADAR011299 is a gene ID. In your case, it should work with 
ADAR011299-PA.
metazoa.ensembl.org/Anopheles_darlingi/Gene/Compara_Tree?db=core;g=ADAR011299

For some species, gene IDs and protein IDs are often identical, which 
can be quite confusing.

Best regards,
Matthieu

On 18/12/12 10:12, Moretti Sébastien wrote:
> Hi
>
> with ensembl API 69, or previous APIs, I used to get a leaf object with
> this function:
>      my $leaf = $tree->find_leaf_by_name($seq_name);
>      print $leaf->node_id;
>
> I've never got problems with ensembl vertebrate data.
>
>
> I tried the same script with Ensembl Metazoa and got this error message:
>      Can't call method "node_id" on an undefined value
> or
>      Use of uninitialized value $leaf in concatenation
> $leaf appears to be undefined, find_leaf_by_name returns undef.
>
>
> Do you have an explanation for this ?
> Regards
>
> e.g.
>      my $leaf = $tree->find_leaf_by_name('ADAR011299');
>      in EMGT00050000000001 gene family
>