def test_genome_halving_only_rearrangements_post_wgd():
param = simulator.SimParameters(wgd_type="GH", num_genes=40, num_chr=2, events=[0, 10])
sim = simulator.Simulation(folder=None, sim_parameters=param)
genomes = sim.run_simulation()
assert 2 * len(genomes[0].chromosomes) == len(genomes[2].chromosomes)
assert len(genomes[0].gene_count().keys()) == len(genomes[2].gene_count().keys())
assert str(genomes[0].chromosomes[0]) == str(genomes[1].chromosomes[0]) and \
str(genomes[0].chromosomes[1]) == str(genomes[1].chromosomes[1])
def test_genome_halving_only_deletions_pre_wgd():
param = simulator.SimParameters(wgd_type="GH", num_genes=40, num_chr=2, del_p=[1, 0], indel_length=[3, 0],
events=[10, 0])
sim = simulator.Simulation(folder=None, sim_parameters=param)
genomes = sim.run_simulation()
assert 2 * len(genomes[0].chromosomes) >= len(genomes[1].chromosomes)
assert len(genomes[0].gene_count().keys()) > len(genomes[1].gene_count().keys())
assert len(genomes[1].gene_count().keys()) == len(genomes[2].gene_count().keys())
def test_pipeline_double_distance_with_only_inter_chromosomal_segmental_duplication():
param = simulator.SimParameters(wgd_type="DD", num_genes=40, num_chr=2, duplication_p=[0, 1],
duplication_length=[0, 3], events=[0, 10], inter_p=1)
sim = simulator.Simulation(folder=None, sim_parameters=param)
genomes = sim.run_simulation()
assert 2 * len(genomes[0].chromosomes) == len(genomes[1].chromosomes)
assert len(genomes[0].gene_count().keys()) == len(genomes[1].gene_count().keys())
assert sum(genomes[0].gene_count().values()) < sum(genomes[1].gene_count().values())
def test_pipeline_double_distance_only_deletions():
param = simulator.SimParameters(wgd_type="DD", num_genes=40, num_chr=2, del_p=[0, 1], indel_length=[0, 3],
events=[0, 10])
sim = simulator.Simulation(folder=None, sim_parameters=param)
genomes = sim.run_simulation()
assert 2 * len(genomes[0].chromosomes) >= len(genomes[1].chromosomes)
assert len(genomes[0].gene_count().keys()) >= len(genomes[1].gene_count().keys())
assert 2 * sum(genomes[0].gene_count().values()) > sum(genomes[1].gene_count().values())
def test_genome_halving_only_segmental_duplications_post_wgd():
param = simulator.SimParameters(wgd_type="GH", num_genes=40, num_chr=2, duplication_p=[0, 1],
duplication_length=[0, 3], events=[0, 10])
sim = simulator.Simulation(folder=None, sim_parameters=param)
genomes = sim.run_simulation()
assert 2 * len(genomes[0].chromosomes) == len(genomes[2].chromosomes)
assert len(genomes[0].gene_count().keys()) == len(genomes[1].gene_count().keys())
assert len(genomes[1].gene_count().keys()) == len(genomes[2].gene_count().keys())
assert sum(genomes[0].gene_count().values()) == sum(genomes[1].gene_count().values())
assert 2 * sum(genomes[1].gene_count().values()) < sum(genomes[2].gene_count().values())
from src import simulator
import pyximport
pyximport.install()
from utils import model, dcj
test_sim = simulator.Simulation(folder=None)
# TODO: FIGURE OUT WHETHER OR NOT COPY NUMBER IS CORRECT, MAY HAVE TO MODIFY SOME TESTS FOR THIS IN THE NEAR FUTURE
# UTILITY FUNCTIONS
def gen_genome(genes, chromosomes):
genome = model.Genome.identity(genes, chromosomes)
for chromosome in genome.chromosomes:
chromosome.copy_number = [1] * len(chromosome.gene_order)
return genome
def get_chr(genome, number):
return genome.chromosomes[number].gene_order
def get_copy_number(genome, number):
return genome.chromosomes[number].copy_number
#################################
# BASIC FUNCTIONALITY TESTS #####
#################################