PyOntoQuery

A Python command line utility that retrieves information from an ontology tree (.obo) file.

Note: if you are installing this on Eddie (the University of Edinburgh's cluster) it seems you will need to follow the 'Without conda' instructions for now

Downloading this git repository

You can download the contents of this git repository by running:

git clone https://github.com/baileythegreen/PyOntoQuery.git

This assumes you have git installed. Or, you can click on the Code button in the top right-ish part of this page, next to the About section and choose Download ZIP, which does not.

Dependencies (Python packages)

obonet — Read OBO-formatted ontologies in Python.
networkx — NetworkX is a dependency of obonet.

Setting up environment

With conda

Setting up the environment

The necessary packages and libraries are given in environment.yml. They may be installed with the conda package manager by running:

$ conda env create --prefix ontology --file environment.yml

creates an 'ontology' environment in the current directory, or

$ conda env create --prefix /path/to/another/location/ontology --file environment.yml

creates the environment in another location.

Activating the environment

You can activate this environment with:

$ conda activate ./ontology

if the environment is in your current directory, or

$ conda activate <path to where ever you created it>/ontology

if it is not.

Adding PyOntoQuery to an existing conda environment

Or to add the dependencies to a different (already extant) conda environment:

$ conda install -c biobuilds obonet

(This line will install obonet and all of its dependencies, which will then be everything you need.)

Without conda

obonet

Install the latest release of obonet from PyPI:

$ pip install obonet

NetworkX

Install the latest version of NetworkX:

$ pip install networkx

Install with all optional dependencies:

$ pip install networkx[all]