[ensembl-dev] get_SimpleAlign(-cdna=>1) broken and deprecated?

[Sébastien Moretti]

Hi

With Ensembl API 71, or previous versions, I used to retrieve nucleotide 
(cds) alignments from a GeneTree set with
    $tree->get_SimpleAlign(-cdna=>1);

And related protein alignment with
    $tree->get_SimpleAlign();


Now with Ensembl API 79
    $tree->get_SimpleAlign(-cdna=>1);
also returns the protein alignment (without warning).


I tried
    $tree->get_SimpleAlign(-SEQ_TYPE => 'cds')
or
    $tree->get_SimpleAlign(-SEQ_TYPE => 'cdna')
without much success.


So what is the proper way now to retrieve a nucleotide alignment from a 
GeneTree set?

Also Bio::EnsEMBL::Compara::GeneTreeNode::get_SimpleAlign is labeled as 
"deprecated soon".


Regards

-- 
Sébastien Moretti
Staff Scientist
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/