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

Matthieu Muffato muffato at ebi.ac.uk
Tue Mar 31 10:47:47 BST 2015


Hi Sébastien,

get_SimpleAlign(-SEQ_TYPE => 'cds') should work. Are you querying the 
live database or your own mirror ? If the latter, have you loaded the 
"other_member_sequence" table ?

Yes, $gene_tree_node->get_SimpleAlign() is likely to be deprecated at 
some point. Instead, 
$gene_tree_node->get_AlignedMemberSet()->get_SimpleAlign() will work

Matthieu

On 31/03/15 08:04, Sébastien Moretti wrote:
> 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
>

-- 
Matthieu Muffato, Ph.D.
Ensembl Compara and TreeFam Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus, Hinxton
Cambridge, CB10 1SD, United Kingdom
Room  A3-145
Phone + 44 (0) 1223 49 4631
Fax   + 44 (0) 1223 49 4468




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