def setUp(self):
self.fsc = fsc2.Fsc2Handler(
name="test-one",
fsc2_path="fsc",
working_directory=FSC_DATA_DIR,
is_calculate_single_population_sfs=True,
is_calculate_joint_population_sfs=True,
is_unfolded_site_frequency_spectrum=False,
is_infinite_sites_model=True,
)
def get_fsc_handler(self, is_unfolded_site_frequency_spectrum):
fsc_handler = fsc2.Fsc2Handler(
name="test-one",
fsc2_path="fsc",
working_directory=FSC_DATA_DIR,
is_calculate_single_population_sfs=True,
is_calculate_joint_population_sfs=True,
is_infinite_sites_model=False,
is_unfolded_site_frequency_spectrum=
is_unfolded_site_frequency_spectrum,
)
return fsc_handler
def test_fsc_config(self):
fsc_handler = fsc2.Fsc2Handler(
name="test-one",
fsc2_path="fsc",
working_directory=FSC_DATA_DIR,
is_calculate_single_population_sfs=True,
is_calculate_joint_population_sfs=True,
is_unfolded_site_frequency_spectrum=False,
is_infinite_sites_model=False,
)
fsc2_config_d = {
"d0_population_size": "Test-1",
"d1_population_size": "Test-2",
"d0_sample_size": "Test-3",
"d1_sample_size": "Test-4",
"div_time": "Test-5",
"num_sites": "Test-6",
"recombination_rate": "Test-7",
"mutation_rate": "Test-8",
"ti_proportional_bias": "Test-9",
"fsc2_command": "test",
}
dest = StringIO()
fsc_handler._write_parameter_configuration(dest=dest,
fsc2_config_d=fsc2_config_d)
result = [row for row in dest.getvalue().split("\n") if row]
# expected = re.sub(r"{[A-Za-z0-9_]+}", "#Test#", fsc2.FSC2_CONFIG_TEMPLATE)
expected = [
"// Number of population samples (demes)", "2",
"// Population effective sizes (number of genes)", "Test-1",
"Test-2", "// Sample sizes", "Test-3", "Test-4",
"// Growth rates: negative growth implies population expansion",
"0", "0",
"// Number of migration matrices : 0 implies no migration between demes",
"0",
"// Historical event: time, source, sink, migrants, new size, new growth rate, migr. matrix 4 historical event",
"1 historical event", "Test-5 0 1 1 2 0 0",
"// Number of independent loci [chromosome]; '0' => same structure for all loci",
"1 0",
"// Per chromosome: Number of contiguous linkage Block: a block is a set of contiguous loci",
"1",
"// Per Block:data type, number of loci, per generation recombination rate, per generation mutation rate and optional parameters",
"DNA Test-6 Test-7 Test-8 Test-9", "// Command: test"
]
self.assertEqual(len(expected), len(result))
for v1, v2 in zip(expected, result):
self.assertEqual(v1, v2)
def __init__(self,
name,
model,
task_queue,
results_queue,
fsc2_path,
working_directory,
run_logger,
logging_frequency,
messenger_lock,
random_seed,
is_calculate_single_population_sfs,
is_calculate_joint_population_sfs,
is_unfolded_site_frequency_spectrum,
is_infinite_sites_model,
is_concatenate_loci,
is_normalize_by_concatenated_num_loci,
is_normalize_by_site_counts,
stat_label_prefix,
is_include_model_id_field,
supplemental_labels,
is_debug_mode,
is_store_raw_alignment,
is_store_raw_mutation_tree,
is_store_raw_true_tree,
raw_data_output_prefix,
raw_data_alignment_format,
raw_data_tree_format,
):
multiprocessing.Process.__init__(self, name=name)
self.model = model
self.rng = random.Random(random_seed)
self.task_queue = task_queue
self.results_queue = results_queue
self.run_logger = run_logger
self.logging_frequency = logging_frequency
self.messenger_lock = messenger_lock
self.is_unfolded_site_frequency_spectrum = is_unfolded_site_frequency_spectrum
self.stat_label_prefix = stat_label_prefix
self.is_include_model_id_field = is_include_model_id_field
self.supplemental_labels = supplemental_labels
self.is_debug_mode = is_debug_mode
self.kill_received = False
self.num_tasks_received = 0
self.num_tasks_completed = 0
self.is_store_raw_alignment = is_store_raw_alignment
# self.is_store_concatenated_alignment = True # TODO
self.is_concatenate_loci = is_concatenate_loci
self.is_normalize_by_concatenated_num_loci = is_normalize_by_concatenated_num_loci
self.is_store_raw_mutation_tree = is_store_raw_mutation_tree
self.is_store_raw_true_tree = is_store_raw_true_tree
self.raw_data_output_prefix = raw_data_output_prefix
self.raw_data_alignment_format = raw_data_alignment_format
self.raw_data_tree_format = raw_data_tree_format
self.is_normalize_by_site_counts = is_normalize_by_site_counts,
self.fsc2_handler = fsc2.Fsc2Handler(
name=name,
fsc2_path=fsc2_path,
working_directory=working_directory,
is_calculate_single_population_sfs=is_calculate_single_population_sfs,
is_calculate_joint_population_sfs=is_calculate_joint_population_sfs,
is_unfolded_site_frequency_spectrum=is_unfolded_site_frequency_spectrum,
is_infinite_sites_model=is_infinite_sites_model,
is_store_raw_alignment=self.is_store_raw_alignment,
is_store_raw_mutation_tree=self.is_store_raw_mutation_tree,
is_store_raw_true_tree=self.is_store_raw_true_tree,
raw_data_alignment_format=self.raw_data_alignment_format,
raw_data_tree_format=self.raw_data_tree_format,
is_debug_mode=self.is_debug_mode,
fsc2_params_adjustment_hack=model.fsc2_params_adjustment_hack
)