obo-parser

A Python library for parsing OBO(Open Biological and Biomedical Ontologies) files.

Installation

pip install obo_parser

Usage

Use in Command Line

obo_parser headers -f path/to/obo_file.obo
obo_parser headers -f path/to/obo_file.obo -o headers.json

obo_parser terms -f path/to/obo_file.obo
obo_parser terms -f path/to/obo_file.obo -o terms.jl

Use in Python

from obo_parser.parser import OBO_Parser

obo = OBO_Parser('./hp.obo')
print(obo.headers)

for term in obo.terms:
    print(term)

    # accessing term attribute
    print(term.id, term.name)
    print(term['id'], term['name'])
    print(term.get('id'), term.get('name'))

    # accessing term dict
    print(term._data)
    print(dict(term))