def initiate_infection(cls, poi):
genomes = []
for _ in range(poi):
genome = Genome.from_reference()
genome.genome = genome.genome + _
genome.id = _
genomes.append(genome)
return genomes
def distribution_simulation(cls,
poi,
strain_differential,
n_events=5,
backcross=False):
genome_pool = Infection.initiate_infection(poi)
parental_genome = genome_pool[0]
unrelated_genome = Genome.from_reference()
unrelated_genome.genome = unrelated_genome.genome - 1.
unrelated_genome.id = -1
print 'parental_genomeID ', parental_genome.id
host = Infection(genome_pool)
data = []
for _ in range(n_events):
print 'event ' + str(_ + 1)
n_oocysts = sample_n_oocysts_function()
n_ihepatocytes = sample_n_hepatocytes_function()
weights = obtain_dirichlet_exponential_strain_proportions(
strain_differential, len(host.unique_genome_pool))
transmission = Infection.mosquito_transmission(
host.unique_genome_pool, n_oocysts, n_ihepatocytes, weights)
#transmission.interpret_ihep_relationships()
transmission.calculate_observable_relatedness()
#transmission.calculate_ibd_stats()
data.append(transmission.return_stats())
if backcross:
if backcross == 1:
transmission.add_strain(parental_genome)
elif backcross == 2:
if _ > 0:
print 'adding unrelated_gnome'
transmission.add_strain(unrelated_genome)
host = transmission
return data