[ensembl-dev] Failed to get Ensembl genes with the API

[mag]

Hi Sébastien,

Ports 5306 and 3306 are indeed similar and return the same results.
Same for mus_musculus versus mus musculus, both are recognised aliases 
for the mouse database (as are mmusculus and mouse).

I have tried various combinations of the above but am unable to 
reproduce your issue.
The only explanation that I can think of is that you are somehow 
connecting to the wrong server/database.
Could you share any more of your script where it deals with the database 
connection, or what happens to the gene adaptor?


Cheers,
mag

On 05/01/2021 12:57, Sebastien Moretti wrote:
> Hi Mag
>
> ports 5306 and 3306 should be similar according to 
> http://www.ensembl.org/info/data/mysql.html
>
> Any differences if 'mus_musculus' is used instead of 'mus musculus'?
>
> Best
> Sébastien
>
>> Hi Mag
>>
>>> Hi Sébastien,
>>>
>>> Thank you for bringing this to our attention.
>>> If you are only wanting to access data for mouse, the 'api' alias 
>>> for git ensembl will provide all the necessary repositories.
>>> You are right however that ensembl-metadata and ensembl-taxonomy 
>>> should be made more easily accessible through our Git tools and we 
>>> will update this in the coming release.
>>
>> Thanks
>>
>>> Regarding your issues retrieving mouse genes, could you provide more 
>>> details on your script?
>>>
>>> The following printed out 56,305.
>>>
>>>     my $registry = "Bio::EnsEMBL::Registry";
>>>
>>>     $registry->load_registry_from_db(
>>>        -db_version => 102,
>>>        -host => 'ensembldb.ensembl.org',
>>>        -user => 'anonymous',
>>>        -port => 3306
>>>     );
>>>
>>>     my $gene_adaptor = $registry->get_adaptor( 'mus musculus', 'Core',
>>>     'Gene' );
>>>
>>>     my $genes = $gene_adaptor->fetch_all();
>>>     print "Found " . scalar(@$genes) . "\n";
>>
>> Our script is similar with API version 102:
>> my $reg = 'Bio::EnsEMBL::Registry';
>> $reg->load_registry_from_db( -user    => 'anonymous',
>>                               -pass    => '',
>>                               -host    => 'ensembldb.ensembl.org',
>>                               -port    => 5306,
>>                               -verbose => 1, # Verbose output
>>                              );
>> my $gene_adaptor = $reg->get_adaptor( 'mus_musculus', 'Core', 'Gene' );
>> my @genes = @{ $gene_adaptor->fetch_all() };
>>
>>
>> The main differences are "mus_musculus" instead of "mus musculus"
>> and port 5306 instead of 3306.
>>
>>
>> Cheers
>> Sébastien
>>
>>> Cheers,
>>> mag
>>>
>>> On 15/12/2020 16:44, Sebastien Moretti wrote:
>>>> Hi
>>>>
>>>> Previously I got all Ensembl gene for a species with the API this way:
>>>> $gene_adaptor = $reg->get_adaptor( 'mus musculus', 'Core', 'Gene' );
>>>>
>>>>
>>>> But it does not look to be so simple with more recent Ensembl API 
>>>> versions.
>>>> First I use the "Git Ensembl tools" but ensembl-metadata and 
>>>> ensembl-taxonomy modules did not come with it for [api].
>>>> According to what is written at 
>>>> http://www.ensembl.org/info/docs/api/api_installation.html I 
>>>> expected them to come with.
>>>>
>>>> http://www.ensembl.org/info/docs/api/api_git.html mentions 
>>>> ensembl-metadata.git but it is not there unless you do
>>>>     git ensembl --clone available
>>>> instead of
>>>>     git ensembl --clone api
>>>>
>>>>
>>>>
>>>> Second what is the right way nowadays to get adaptor for all genes?
>>>> $gene_adaptor = $reg->get_adaptor( 'mus musculus', 'Core', 'Gene' );
>>>> looks to work but returns only a subset of genes (between 20 and 70).
>>>>
>>>> Thanks for your help
>>>>
>>>> -- 
>>>> Sébastien Moretti
>>>> Staff Scientist
>>>> Department of Ecology and Evolution,
>>>> Biophore, University of Lausanne,
>>>> CH-1015 Lausanne, Switzerland
>>>> Tel.: +41 (21) 692 4221/4079
>>>> http://bioinfo.unil.ch/ http://bgee.org/ http://selectome.unil.ch/
>>>>
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