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

[Sebastien Moretti]

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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