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
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.
obonet — Read OBO-formatted ontologies in Python.
networkx — NetworkX is a dependency of obonet.
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.
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.
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.)
Install the latest release of obonet from PyPI:
$ pip install obonet
Install the latest version of NetworkX:
$ pip install networkx
Install with all optional dependencies:
$ pip install networkx[all]