[ensembl-dev] Failed to get Ensembl genes with the API
Sebastien Moretti
smoretti at unil.ch
Fri Dec 18 09:34:30 GMT 2020
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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