def _trials(recon_input: _ReconInput, dup_cost: float, transfer_cost: float,
loss_cost: float, num_trials: int) -> list:
"""
:param recon_input <_ReconInput> - class containing host tree, parasite tree, tip mapping
:param dup_cost <float> - duplication cost
:param transfer_cost <float> - transfer cost
:param loss_cost <float> -loss cost
:param num_trials <int> - number of trials in Monte Carlo simulation
:return: list of floating point costs of reconciliations of the Monte Carlo samples
"""
costs = list() # List of costs of random trials
parasites = recon_input.tip_mapping.keys()
hosts = list(recon_input.tip_mapping.values())
for t in range(num_trials):
random_phi = _create_random_phi(recon_input.tip_mapping)
for p in parasites:
h = random.choice(hosts)
random_phi[p] = h
new_input = _ReconInput(recon_input.host_dict, None,
recon_input.parasite_dict, None, random_phi)
_, cost, _, _ = recongraph_tools.DP(new_input, dup_cost, transfer_cost,
loss_cost)
costs.append(cost)
return costs
def test_write_to_file(self):
recon_input = input_reader._ReconInput(self.example_host, None, self.example_parasite, None,
self.example_valid_mapping)
host_save_path = "./temp_host.tree"
parasite_save_path = "./temp_parasite.tree"
tip_mapping_save_path = "./temp_mapping.mapping"
recon_input.save_to_files(host_save_path, parasite_save_path, tip_mapping_save_path)
os.path.exists(host_save_path)
os.path.exists(parasite_save_path)
os.path.exists(tip_mapping_save_path)
result_input = input_reader._ReconInput.from_files(host_save_path, parasite_save_path, tip_mapping_save_path)
self.assertEqual(self.example_host, result_input.host_dict)
self.assertEqual(self.example_parasite, result_input.parasite_dict)
self.assertEqual(self.example_valid_mapping, result_input.tip_mapping)
os.remove(host_save_path)
os.remove(parasite_save_path)
os.remove(tip_mapping_save_path)
def test_read_invalid_tip_error(self):
recon_input = input_reader._ReconInput()
recon_input.read_host(self.example_host_file)
recon_input.read_parasite(self.example_parasite_file)
self.assertRaises(input_reader.ReconInputError, recon_input.read_mapping, self.example_invalid_mapping_file)
def test_read_success(self):
recon_input = input_reader._ReconInput()
recon_input.read_host(self.example_host_file)
recon_input.read_parasite(self.example_parasite_file)
recon_input.read_mapping(self.example_mapping_file)
self.assertTrue(recon_input.is_complete())
def test_init_success(self):
recon_input = input_reader._ReconInput(self.example_host, None, self.example_parasite, None,
self.example_valid_mapping)
self.assertTrue(recon_input.is_complete())
def test_init_empty(self):
recon_input = input_reader._ReconInput()
self.assertTrue(isinstance(recon_input, input_reader._ReconInput))
self.assertIsNone(recon_input.host_dict)
self.assertIsNone(recon_input.parasite_dict)
self.assertIsNone(recon_input.tip_mapping)