import pyhpo
from pyhpo.parser import diseases
from pyhpo.parser import genes
[docs]
def build_ontology_annotations(
data_folder: str, ontology: "pyhpo.OntologyClass", transitive: bool = False
) -> None:
"""
Builds all annotations and associated genes and diseases
to the HPO terms in the Ontology.
Parameters
----------
data_folder:
The full path to the folder that contains the master data files
ontology:
The ontology of HPO terms
"""
if transitive:
genes._parse_genes_transitive(data_folder)
else:
genes._parse_genes(data_folder)
genes._add_genes_to_ontology(ontology)
diseases._parse_phenotype_hpoa_file(data_folder)
diseases._add_decipher_to_ontology(ontology)
diseases._add_omim_to_ontology(ontology)
diseases._add_orpha_to_ontology(ontology)