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read_disease_yml.py
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read_disease_yml.py
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"""Module to read disease parameters and create a Disease object."""
import yaml
from facs.base.disease import Disease
def read_disease_yml(ymlfile: str) -> Disease:
"""Read disease parameters from a YAML file and create a Disease object."""
with open(ymlfile, "r", encoding="utf-8") as file:
data = yaml.safe_load(file)
print(data)
disease = Disease(
data["infection_rate"],
data["incubation_period"],
data["mild_recovery_period"],
data["recovery_period"],
data["mortality_period"],
data["period_to_hospitalisation"],
data["immunity_duration"],
data["immunity_fraction"],
)
disease.add_mortality_chances(data["mortality"])
disease.add_hospitalisation_chances(data["hospitalised"])
if "mutations" in data:
# Handle mutations
disease.add_mutations(data["mutations"])
elif "genotypes" in data:
# Handle genotypes
disease.add_genotypes(data["genotypes"])
else:
print("No mutations or genotypes provided")
print(disease)
return disease