W43GVG / Ensembl-CLI

CLI interface for Ensembl queries.

Ensembl-CLI

CLI interface for Ensembl queries

Presentation

The objective is to implement the possibilities offered by Ensembl's REST API in a command line application.

Use

git clone https://github.com/W43GVG/Ensembl-CLI

Query

python ensembl-cli.py COMMANDS

Get help

python ensembl-cli.py COMMAND --help

Ontologies

Multiple ontologies can be obtained (gene ontology: GO, sequence ontology: SO, protein ontology: PR, uberon: UBERON).

python ensembl-cli.py onto_id 0000370 SO json

Search ontological terms:

python ensembl-cli.py onto_name TERM FORMAT

Example:

python ensembl-cli.py onto_name tubulin json

License, notes

W43GVG under the MIT License.

Yates, Andrew et al. “The Ensembl REST API: Ensembl Data for Any Language.” Bioinformatics 31.1 (2014): 143–145.