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

[Matthieu Muffato]

Hi Sébastien,

I'm afraid I can't reproduce the error. I can run the attached script 
with the release/79 branch and it prints both protein and nucleotide 
alignments. The script is what you've pasted in your email.

How does my script behave in your environment ?

Matthieu

On 31/03/15 11:23, Sébastien Moretti wrote:
> Hi Matthieu,
>
> I use the live database and in my hands
>      get_SimpleAlign(-SEQ_TYPE => 'cds')
> or
>      get_AlignedMemberSet()->get_SimpleAlign(-SEQ_TYPE => 'cds')
> return both the protein alignment.
> I cannot get the nucleotide alignment.
>
>
> Thanks for your help
>
>
> my $reg = 'Bio::EnsEMBL::Registry';
> $reg->load_registry_from_db(
>       ...
> );
> my $tree_adaptor = $reg->get_adaptor('Multi', 'compara', 'GeneTree');
> my $tree = $tree_adaptor->fetch_by_root_id(375021); # id example
> $tree    = $tree->root; # To use GeneTreeNode everywhere after that !!!!
> ...
> my $prot_align = $tree->get_AlignedMemberSet()->get_SimpleAlign();
> my $cds_align  =
> $tree->get_AlignedMemberSet()->get_SimpleAlign(-SEQ_TYPE => 'cds');
>
>> 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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