[ensembl-dev] find_leaf_by_name in ensembl Metazoa

[Moretti Sébastien]

Hi Matthieu

you mean I can do something like
     $tree->find_leaf_by_name($seq_name) || 
$tree->find_leaf_by_name($seq_name.'-PA');

In other words, adding -PA in all failed cases will fix my problem ?

> 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
-- 
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/