示例#1
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    def get_from_parent_and_environment(self):  # parental inheritance and environmental acquisition
        parental_contribution = []
        for i in range(self.number_of_host_in_population):  # select parent for next generation
            rnd = random.randint(0, self.number_of_environmental_species - 1)
            parental_contribution.append(
                self.composition_of_individual[rnd].microbiome / float(self.number_of_microbes_in_host))
            self.composition_of_individual[rnd].microbiome *= 2
        environmental_contribution = addition_of_arrays(
            self.percentage_of_pooled_environmental_component,
            1 - self.percentage_of_pooled_environmental_component,
            self.microbiome_sum, self.environment)  # mix pooled and fixed env

        for i in range(self.number_of_host_in_population):  # mix environmental and parental contribution
            mixed_contribution = addition_of_arrays(
                1 - self.percentage_of_environmental_acquisition,
                self.percentage_of_environmental_acquisition,
                parental_contribution[i], environmental_contribution)

            self.composition_of_individual[i].microbiome = numpy.random.multinomial(
                self.number_of_microbes_in_host, mixed_contribution / sum(mixed_contribution))
示例#2
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 def sum_species(self):
     self.microbiome_sum = numpy.array([])
     for individual in self.composition_of_individual:
         self.microbiome_sum = addition_of_arrays(1, 1, self.microbiome_sum, individual.microbiome)
     self.microbiome_sum = self.microbiome_sum / float(sum(self.microbiome_sum))  # composition of the microbiomes within the population in terms of genome
     self.species_community = self.microbiome_sum  # composition of the microbiomes within the population in terms of species marker