def print_hpo(out_dir):
"""Print HPO files to a directory
Args:
out_dir(Path)
"""
hpo_file_name = "hpo.obo"
hpo_file_path = out_dir / hpo_file_name
LOG.info("Download HPO terms to %s", hpo_file_path)
with hpo_file_path.open("w", encoding="utf-8") as outfile:
for line in fetch_hpo_terms():
outfile.write(line + "\n")
hpo_file_name = "ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt"
hpo_file_path = out_dir / hpo_file_name
LOG.info("Download HPO genes to %s", hpo_file_path)
with hpo_file_path.open("w", encoding="utf-8") as outfile:
for line in fetch_hpo_genes():
outfile.write(line + "\n")
hpo_file_name = "ALL_SOURCES_ALL_FREQUENCIES_phenotype_to_genes.txt"
hpo_file_path = out_dir / hpo_file_name
LOG.info("Download HPO TO genes to %s", hpo_file_path)
with hpo_file_path.open("w", encoding="utf-8") as outfile:
for line in fetch_hpo_to_genes():
outfile.write(line + "\n")
hpo_file_name = "ALL_SOURCES_ALL_FREQUENCIES_diseases_to_genes_to_phenotypes.txt"
hpo_file_path = out_dir / hpo_file_name
LOG.info("Download HPO disease %s", hpo_file_path)
with hpo_file_path.open("w", encoding="utf-8") as outfile:
for line in fetch_hpo_phenotype_to_terms():
outfile.write(line + "\n")
def get_reduced_hpo_terms(hpo_terms):
"""Return a reduced version of the hpo terms
Args:
hpo_terms(set(str)): Set of choosen terms that should be included
Yields:
hpo_line: A line with hpo information
"""
hpo_lines = fetch_hpo_terms()
begining = True
term_lines = []
# We want to keep the header lines
keep = True
nr_terms = 0
nr_kept = 0
for line in hpo_lines:
# When we encounter a new term we yield all lines of the previous term
if line.startswith("[Term]"):
nr_terms += 1
if keep:
nr_kept += 1
for hpo_line in term_lines:
yield hpo_line
keep = False
term_lines = []
elif line.startswith("id"):
hpo_id = line[4:]
if hpo_id in hpo_terms:
keep = True
term_lines.append(line)
if keep:
for hpo_line in term_lines:
yield hpo_line
LOG.info("Nr of terms in file %s", nr_terms)
LOG.info("Nr of terms kept: %s", nr_kept)
def test_fetch_hpo(hpo_terms_file):
"""Test fetch resource"""
# GIVEN an URL
url = "https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo"
with open(hpo_terms_file, "r") as hpo_file:
content = hpo_file.read()
responses.add(
responses.GET,
url,
body=content,
status=200,
)
# WHEN fetching the resource
data = scout_requests.fetch_hpo_terms()
# THEN assert that the HPO header is there
assert "format-version" in data[0]
def test_fetch_hpo(hpo_terms_file):
"""Test fetch resource"""
# GIVEN an URL
url = "http://purl.obolibrary.org/obo/hp.obo"
with open(hpo_terms_file, "r") as hpo_file:
content = hpo_file.read()
responses.add(
responses.GET,
url,
body=content,
status=200,
)
# WHEN fetching the resource
data = scout_requests.fetch_hpo_terms()
# THEN assert that the HPO header is there
assert "format-version" in data[0]
def load_hpo(
adapter,
disease_lines=None,
hpo_lines=None,
hpo_gene_lines=None,
):
"""Load the hpo terms and hpo diseases into database
Args:
adapter(MongoAdapter)
disease_lines(iterable(str)): These are the omim genemap2 information
hpo_lines(iterable(str)): lines from file http://purl.obolibrary.org/obo/hp.obo
hpo_gene_lines(iterable(str)): lines from file
https://ci.monarchinitiative.org/view/hpo/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/phenotype_to_genes.txt
"""
# Create a map from gene aliases to gene objects
alias_genes = adapter.genes_by_alias()
# Fetch the hpo terms if no file
if not hpo_lines:
hpo_lines = fetch_hpo_terms()
# Fetch the hpo gene information if no file
if not hpo_gene_lines:
hpo_gene_lines = fetch_hpo_to_genes_to_disease()
load_hpo_terms(adapter, hpo_lines, hpo_gene_lines, alias_genes)
if not disease_lines:
LOG.warning("No omim information, skipping to load disease terms")
return
load_disease_terms(
adapter=adapter,
genemap_lines=disease_lines,
genes=alias_genes,
hpo_disease_lines=hpo_gene_lines,
)
def load_hpo_terms(adapter,
hpo_lines=None,
hpo_gene_lines=None,
alias_genes=None):
"""Load the hpo terms into the database
Parse the hpo lines, build the objects and add them to the database
Args:
adapter(MongoAdapter)
hpo_lines(iterable(str)): lines from file http://purl.obolibrary.org/obo/hp.obo
hpo_gene_lines(iterable(str)): lines from file
https://ci.monarchinitiative.org/view/hpo/job/hpo.annotations/lastSuccessfulBuild/artifact/rare-diseases/util/annotation/phenotype_to_genes.txt
alias_genes
"""
# Fetch the hpo terms if no file
if not hpo_lines:
hpo_lines = fetch_hpo_terms()
# Parse the terms
LOG.info("Parsing hpo terms")
hpo_terms = build_hpo_tree(hpo_lines)
# Fetch the hpo gene information if no file
if not hpo_gene_lines:
hpo_gene_lines = fetch_hpo_to_genes_to_disease()
# Get a map with hgnc symbols to hgnc ids from scout
if not alias_genes:
alias_genes = adapter.genes_by_alias()
LOG.info("Adding gene information to hpo terms ...")
for hpo_to_symbol in parse_hpo_to_genes(hpo_gene_lines):
hgnc_symbol = hpo_to_symbol["hgnc_symbol"]
hpo_id = hpo_to_symbol["hpo_id"]
# Fetch gene info to get correct hgnc id
gene_info = alias_genes.get(hgnc_symbol)
if not gene_info:
continue
hgnc_id = gene_info["true"]
if hpo_id not in hpo_terms:
continue
hpo_term = hpo_terms[hpo_id]
if not "genes" in hpo_term:
hpo_term["genes"] = set()
hpo_term["genes"].add(hgnc_id)
start_time = datetime.now()
LOG.info("Loading the hpo terms...")
nr_terms = len(hpo_terms)
hpo_bulk = []
with progressbar(hpo_terms.values(),
label="Loading hpo terms",
length=nr_terms) as bar:
for hpo_info in bar:
hpo_bulk.append(build_hpo_term(hpo_info))
if len(hpo_bulk) > 10000:
adapter.load_hpo_bulk(hpo_bulk)
hpo_bulk = []
if hpo_bulk:
adapter.load_hpo_bulk(hpo_bulk)
LOG.info("Loading done. Nr of terms loaded {0}".format(nr_terms))
LOG.info("Time to load terms: {0}".format(datetime.now() - start_time))
all_ancestors = get_all_ancestors(hpo_tree, term, set())
term["all_ancestors"] = all_ancestors
return hpo_tree
if __name__ == "__main__":
import sys
from pprint import pprint as pp
from scout.utils.handle import get_file_handle
from scout.utils.scout_requests import fetch_hpo_terms
if not len(sys.argv) > 1:
file_handle = fetch_hpo_terms()
else:
file_handle = get_file_handle(sys.argv[1])
hpo_tree = build_hpo_tree(file_handle)
my_term = hpo_tree["HP:0200024"]
pp(my_term)
# print(get_all_ancestors(hpo_tree, my_term))
for term in hpo_tree:
pp(hpo_tree[term])
# phenotypes = parse_hpo_phenotypes(file_handle)
# for hpo_id in phenotypes:
# hpo_term = phenotypes[hpo_id]