def simulate_double_distance_instance(genome_parameters, dist_parameters,
path_to_dir):
current_insertion_gene = genome_parameters.num_genes + 1
predup_genome = Genome.identity(genome_parameters.num_genes,
genome_parameters.num_chr,
name="R")
a_genome, _, _ = simulate_distance_with_wgd(
source_genome=predup_genome,
dist_parameters=dist_parameters,
current_insertion_gene=current_insertion_gene,
name="A")
save_simulation([predup_genome, a_genome], path_to_dir)
def simulate_median_instance(genome_parameters, dist_parameters, path_to_dir):
current_insertion_gene = genome_parameters.num_genes + 1
median_genome = Genome.identity(genome_parameters.num_genes,
genome_parameters.num_chr,
name="median")
genomes = []
for i in range(3):
genome, _, current_ins_gene = simulate_regular_distance(
source_genome=median_genome,
dist_parameters=dist_parameters,
current_insertion_gene=current_insertion_gene,
name="P" + str(i + 1))
genomes.append(genome)
current_insertion_gene = current_ins_gene
genomes.append(median_genome)
save_simulation(genomes, path_to_dir)
def simulate_guided_halving_instance(genome_parameters, dist_parameters_before,
dist_parameters_after, path_to_dir):
current_insertion_gene = genome_parameters.num_genes + 1
b_genome = Genome.identity(genome_parameters.num_genes,
genome_parameters.num_chr,
name="B")
predup_genome, _, current_ins_gene = simulate_regular_distance(
source_genome=b_genome,
dist_parameters=dist_parameters_before,
current_insertion_gene=current_insertion_gene,
name="R")
a_genome, _, _ = simulate_distance_with_wgd(
source_genome=predup_genome,
dist_parameters=dist_parameters_after,
current_insertion_gene=current_insertion_gene,
name="A")
save_simulation([b_genome, predup_genome, a_genome], path_to_dir)
