[ensembl-dev] get_SimpleAlign problem with cdna

[Matthieu Muffato]

Hi Sébastien

The documentation is indeed confusing and needs some rephrasing.
"clusterset_id" does not have a default value in fetch_all(). The value 
"default" must be given to retrieve the default trees

Regards,
Matthieu

On 20/08/12 10:24, Moretti Sébastien wrote:
> Hi Matthieu
>
> it works as expected now, thanks.
>
>
> http://www.ensembl.org/info/docs/Doxygen/compara-api/classBio_1_1EnsEMBL_1_1Compara_1_1DBSQL_1_1GeneTreeAdaptor.html#a4907fd3f16cd5da965038229e6b18247
>
> The current documentation shows this:
> Arg [-CLUSTERSET_ID] (opt)
>               : string: the name of the clusterset (default is "default")
>
> So,   -clusterset_id => 'default'   should really be optional, but it is
> not ?
>
>> Hi Sébastien
>>
>> Your initial way of sorting trees by stable_id is actually ok.
>>
>> Can you add the "-clusterset_id => 'default'" to the fetch_all() call ?
>> On top of the default, usual, gene trees, we now store the other trees
>> computed by TreeBest (phyml, neighbour-joining) and fetch_all() returns
>> all of them
>>
>> Regards,
>> Matthieu


-- 
Matthieu Muffato, Ph.D.
Ensembl Developer - Comparative Genomics
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom