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

[Sébastien Moretti]

Hi Matthieu,

It works now!
In fact I had a second
    get_SimpleAlign(-cdna=>1)
overriding the replaced
    get_AlignedMemberSet()->get_SimpleAlign(-SEQ_TYPE => 'cds')
when I filter out some genes or nodes in the tree.

It was faster/simpler to recall get_SimpleAlign() on this filtered GeneSet.

Now both get_SimpleAlign use 
get_AlignedMemberSet()->get_SimpleAlign(-SEQ_TYPE => 'cds');


You should add a warning when people use get_SimpleAlign(-cdna=>1)
because currently it goes back to default (protein alignment) and does 
not return what (was) expected.


Thanks for your help.

> 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

-- 
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/