import csv
import os
from typing import Set
from pyhpo.annotations import Gene, GeneSingleton
from pyhpo.parser.generics import id_from_string, remove_outcommented_rows
import pyhpo
FILENAME = "phenotype_to_genes.txt"
# Cloumn mappings in phenotype_to_genes file
HPO_ID = 0
HGNC_ID = 2
GENE_SYMBOL = 3
def _parse_phenotype_to_gene_file(path: str) -> None:
Gene.clear()
filename = os.path.join(path, FILENAME)
with open(filename) as fh:
reader = csv.reader(
remove_outcommented_rows(remove_outcommented_rows(fh), ignorechar="hpo_id"),
delimiter="\t",
)
for cols in reader:
gene = Gene(hgncid=int(cols[HGNC_ID]), symbol=cols[GENE_SYMBOL])
gene.hpo.add(id_from_string(cols[HPO_ID]))
def _add_genes_to_ontology(ontology: "pyhpo.OntologyClass") -> None:
ontology._genes = all_genes()
for gene in ontology._genes:
for term_id in gene.hpo:
add_gene_to_term(gene, ontology[term_id])
[docs]
def add_gene_to_term(
gene: "pyhpo.annotations.GeneSingleton", term: "pyhpo.HPOTerm"
) -> None:
"""
Recursive function to add Gene to an HPOTerm and all its parents
Parameters
----------
gene:
Gene to add to term
term:
HPOTerm that is associated with the gene
"""
if gene in term.genes:
return None
term.genes.add(gene)
for parent in term.parents:
add_gene_to_term(gene, parent)
return None
[docs]
def all_genes() -> Set["GeneSingleton"]:
return set(Gene.keys())