[ensembl-dev] find_leaf_by_name in ensembl Metazoa

[Moretti Sébastien]

So, here is what I did:

my $member_adaptor = $reg->get_adaptor('metazoa', 'compara', 'Member');
my $gene_member    = 
$member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE', $seq_name);
my $peptide_member = $gene_member->get_canonical_Member();
my $leaf = $tree->find_leaf_by_name($peptide_member->stable_id);


It works for some genes that previously failed, but now it stops with 
this new error message:
     Can't call method "get_canonical_Member" on an undefined value
This is for gene EHJ66117, always in EMGT00050000000001 gene tree.


> Hi Sébastien
>
> It works for this gene, but I'm not even sure it would work for all the
> genes of that species. And the rule may be even different for other
> species.
>
> A safer way is to use API to translate gene IDs to protein IDs. We are
> actually only interested in the protein used to build the gene tree (the
> "canonical" protein) and not all the possible translations.
>
> my $gene_member =
> $member_adaptor->fetch_by_source_stable_id('ENSEMBLGENE', 'ADAR011299');
> my $peptide_member = $gene_member->get_canonical_Member();
>
> $tree->find_leaf_by_name($peptide_member->stable_id);
>
> This should work for any species, and both on Ensembl and Ensembl Genomes.
>
> Matthieu
>
> On 18/12/12 10:43, Moretti Sébastien wrote:
>> 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/