[ensembl-dev] get_SimpleAlign problem with cdna

[Moretti Sébastien]

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
-- 
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/