def test_no_hpo_config_option(self):
config.remove_option('hpo', 'disease_to_phenotype_file')
phenotypes = [
['HP:0012759', 'HP:0003011', 'HP:0011442'],
['HP:0012759', 'HP:0003011'],
]
with self.assertRaises(NoOptionError):
predict_likelihood_moldx(phenotypes)
def test_no_hpo_config_section(self):
config.remove_section('hpo')
phenotypes = [
['HP:0012759', 'HP:0003011', 'HP:0011442'],
['HP:0012759', 'HP:0003011'],
]
with self.assertRaises(NoSectionError):
predict_likelihood_moldx(phenotypes)
def test_bad_k(self):
phenotypes = [
['HP:0012759', 'HP:0003011', 'HP:0011442'],
['HP:0012759', 'HP:0003011'],
]
with self.assertRaises(KeyError):
predict_likelihood_moldx(
phenotypes,
self.phenotype_groups,
self.hpo_network,
self.alt2prim,
k_phenotype_groups=500
)
def test_predict_likelihood_phenotypes_only(self):
phenotypes = [
['HP:0012759', 'HP:0003011', 'HP:0011442'],
['HP:0012759', 'HP:0003011'],
]
probabilities = predict_likelihood_moldx(phenotypes)
self.assertAlmostEqual(probabilities[0], 0.33, places=2)
def test_predict_likelihood(self):
phenotypes = [
['HP:0012759', 'HP:0003011', 'HP:0011442'],
['HP:0012759', 'HP:0003011'],
]
probabilities = predict_likelihood_moldx(phenotypes, self.phenotype_groups, self.hpo_network, self.alt2prim)
self.assertAlmostEqual(probabilities[0], 0.33, places=2)
def likelihood_moldx(input_file, output_file=None, k_phenotype_groups=1000):
"""
:param input_file: The file path to a file containing three columns. [ID\tkey=value\thpodid,hpoid,hpoid]
:param output_file: The file path to an output file containing the predicted probabilities
:param k_phenotype_groups: The number of phenotype groups to use for encoding phenotypes. The CLI version of phenopy allows for one of [1000, 1500]
"""
try:
obo_file = config.get('hpo', 'obo_file')
except (NoSectionError, NoOptionError):
logger.critical(
'No HPO OBO file found in the configuration file. See "hpo:obo_file" parameter.'
)
sys.exit(1)
try:
disease_to_phenotype_file = config.get('hpo',
'disease_to_phenotype_file')
except (NoSectionError, NoOptionError):
logger.critical(
'No HPO annotated dataset file found in the configuration file.'
' See "hpo:disease_to_phenotype_file" parameter.')
sys.exit(1)
logger.info(f'Loading HPO OBO file: {obo_file}')
hpo_network, alt2prim, _ = \
generate_annotated_hpo_network(obo_file,
disease_to_phenotype_file,
)
# parse input records
input_records = parse_input(input_file, hpo_network, alt2prim)
record_ids = [record["record_id"] for record in input_records]
phenotypes = [record["terms"] for record in input_records]
# predict likelihood of molecular diagnosis
positive_probabilities = predict_likelihood_moldx(
phenotypes,
phenotype_groups=None,
hpo_network=hpo_network,
alt2prim=alt2prim,
k_phenotype_groups=k_phenotype_groups,
)
if output_file is None:
output_file = "phenopy.likelihood_moldx.txt"
try:
with open(output_file, "w") as f:
for sample_id, probability in zip(record_ids,
positive_probabilities):
f.write(f"{sample_id}\t{probability}\n")
except IOError:
sys.exit("Something went wrong writing the probabilities to file")