EnsemQuery is a command line tool that serves as a convenient interface for fetching and saving specific genetic data points from Ensembl endpoints. Designed with extensibility in mind, the tool is currently focused on the VEP endpoint but aims to incorporate other Ensembl services in the future. It's a useful utility for researchers, healthcare professionals, and anyone interested in genetic data analysis.
- Python 3.10 or higher
- Poetry for dependency management
- Clone the repository:
git clone git@github.com:Tiffany8/EnsemQuery.git
- Navigate to the project directory:
cd EnsemQuery
- Install the package using Poetry:
poetry install
- Activate the virtual environment:
poetry shell
- Now you can run the CLI tool:
eqry --help
- This only works if you don't have 2fa setup on your github account (though, I do recomend 2fa setup 😅)
poetry add git+https://[username]:[password]@github.com/tiffany8/EnsemQuery.git
eqry --help
** Note: currently only one, vep, is available
eqry vep --help
Get variant consequences from ids (Note: a variants.txt can be found here)
eqry vep ids variants.txt
eqry vep ids variants.txt --output-fn mycustomfilename.tsv
eqry vep ids variants.txt --output-fn=mycustomfilename.tsv --output-dir=/complete/path/to/existing/folder
- Setup environment
poetry shell
poetry install
- Run tests
- To run all tests (note '-s' flag needed to for stdout)
pytest -s
- To run unittests
pytest -m "not e2e"
- To run e2e tests
pytest -m e2e -s
This is my kanban I used to track work (link expires 9/26/23).