A few scripts to test runoak on PomBase data
To install the dependencies, we used poetry (see poetry installation instructions). These scripts work with poetry version 1.4.2, to update you can do poetry self update.
In the source directory run:
poetry install
This should create a folder .venv with the python virtual environment. To activate the virtual environment, then run:
poetry shell
Now when you call python, it will be the one from the .venv.
Execute the bash script get_data.sh, see the comments to see what the script does.
To run the enrichments, see example_enrichment.sh. Full documentation on how to run the enrichment can be found here.
- Taxon constrains: there is no need to run taxon constrains, as terms with less than two annotations from the GO ontology are excluded from the analysis. There are some edge cases, discussed in this issue.