Parses ontologies in .obo format (such as the Human Phenotype Ontology) and converts them to a .tsv table.

Install

git clone https://github.com/macarthur-lab/obo_parser.git

Test

python -m unittest discover

Run

Examples:

python obo_parser.py --help
python obo_parser.py -r HP:0000118 http://purl.obolibrary.org/obo/hp.obo -o hpo.tsv
python obo_parser.py -c -r HP:0000118 http://purl.obolibrary.org/obo/hp.obo | cut -f 1,2,4,5,10,11 > hp.tsv