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

Sebastien Moretti smoretti at unil.ch
Tue Dec 15 16:44:06 GMT 2020


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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