def add_genes(cb):
# Add genes
genes = {
'arabiensis': [{
"Alleles": {
"a0": 1.0
},
"Mutations": {}
}],
'funestus': [{
"Alleles": {
"b1": 1.0,
"b0": 0.0
},
"Mutations": {
"b1:b0": 0.0,
"b0:b1": 0.0
}
}],
}
set_species_genes(cb, genes)
# Add gene trait modifiers
traits = {
'funestus': [{
"Allele_Combinations": [["b1", "b1"]],
"Trait_Modifiers": {
"MORTALITY": 100
}
}, {
"Allele_Combinations": [["b0", "b0"]],
"Trait_Modifiers": {
"MORTALITY": 1
}
}]
}
set_species_trait_modifiers(cb, traits)
return None
'logLevel_Simulation': 'ERROR',
'logLevel_StandardEventCoordinator': 'ERROR',
'logLevel_LarvalHabitatMultiplier': 'ERROR',
'logLevel_SimulationEventContext': 'ERROR',
'logLevel_SusceptibilityMalaria': 'ERROR'
})
#################################### VECTOR GENETICS ##############################
# Add genes
genes = {'gambiae': [{
"Alleles": {"a0": 1.0, "a1": 0.0},
"Mutations": {"a1:a0": 0.05}
}]
}
set_species_genes(cb, genes)
release_numbers = [1000]
net_coverages = [0.8]
copy_to_likelihoods = np.arange(1.0, 1.01, 0.1).tolist()
release_nodes = [6]
transmission_probs = [0.3]
start_days = [180]
VC_and_GM = [
[ModFn(DTKConfigBuilder.set_param, 'Run_Number', seed),
ModFn(DTKConfigBuilder.set_param, 'Serialized_Population_Path', ''),
ModFn(add_nets, coverage=net_coverage, number=number, num_nodes=numnodes, start_day=start_day),
ModFn(add_release, number=number, num_nodes=numnodes, start_day=start_day),
ModFn(add_drivers, copy_to_likelihood=likelihood),
ModFn(add_trait_modifiers, transmission_to_human=transmission_prob)
]