def create_merged_bayesian_network_for_event(
event,
prefix,
bayesian_network,
assert_merge_definitions=False,
logger=StdOutLogger(verbose=False)):
merge_def_list = BayesianNetworkMergeUtils.create_merge_definition_list(
event, prefix, merge_singleton_events=False)
logger.log('Merging...', includeTimestamp=True)
logger.set_carriage_reset(True)
count = len(merge_def_list)
for index, merge_def in enumerate(merge_def_list):
logger.log("\rMerging '%s' (%i of %i)" %
(merge_def.get_merged_event(), index + 1, count),
includeTimestamp=True)
merge_defs = DistributionEventMergeDefinitions(
event.name,
bayesian_network,
allow_unspecified_events=True,
assert_merge_definitions=assert_merge_definitions)
merge_defs.set_merge_definitions([merge_def])
bn_wrapper = BayesianNetworkWrapper(bayesian_network)
bayesian_network = bn_wrapper.create_network_with_merged_events(
merge_defs, bake=True)
logger.set_carriage_reset(False)
logger.log('Merging done!', includeTimestamp=True)
return bayesian_network
def test_merge_definitions_3__duplicated_events(bayesian_network_1):
merge_def1 = EventMergeDefinition('V1')
merge_def1.extend(['V1*01', 'V1*02', 'V1*02'])
merge_defs = DistributionEventMergeDefinitions(
'v_gene',
bayesian_network_1,
allow_unspecified_events=True,
assert_merge_definitions=True)
with pytest.raises(ValueError) as e:
merge_defs.set_merge_definitions([merge_def1])
assert str(
e.value) == DistributionEventMergeDefinitions.ERR_DUPLICATE_EVENT_MSG
def test_merge_definitions_2__event_not_found(bayesian_network_1):
merge_def1 = EventMergeDefinition('V1')
merge_def1.extend(['V1*01', 'V1*02', 'V1*04'])
merge_defs = DistributionEventMergeDefinitions(
'v_gene',
bayesian_network_1,
allow_unspecified_events=True,
assert_merge_definitions=True)
with pytest.raises(ValueError) as e:
merge_defs.set_merge_definitions([merge_def1])
assert str(
e.value) == DistributionEventMergeDefinitions.ERR_EVENT_NOT_FOUND
def create_merg_defs(bn):
merge_def1 = EventMergeDefinition('v_choice:TRBV7-2')
merge_def1.extend([
'v_choice:TRBV7-2*01', 'v_choice:TRBV7-2*02', 'v_choice:TRBV7-2*03',
'v_choice:TRBV7-2*04'
])
merge_defs = DistributionEventMergeDefinitions(
'GeneChoice_V_gene_Undefined_side_prio7_size147',
bn,
allow_unspecified_events=True,
assert_merge_definitions=True)
merge_defs.set_merge_definitions([merge_def1])
return merge_defs
def test_merge_definitions_4__unspecified_event(bayesian_network_1):
merge_def1 = EventMergeDefinition('V1')
merge_def1.extend(['V1*01', 'V1*02', 'V1*03'])
merge_defs = DistributionEventMergeDefinitions(
'v_gene',
bayesian_network_1,
allow_unspecified_events=False,
assert_merge_definitions=True)
with pytest.raises(ValueError) as e:
merge_defs.set_merge_definitions([merge_def1])
assert str(
e.value
) == DistributionEventMergeDefinitions.ERR_UNSPECIFIED_EVENTS_NOT_ALLOWED_MSG
def test_merge_definitions_5__one_merge_def_only(bayesian_network_1):
merge_def1 = EventMergeDefinition('V1')
merge_def1.extend(['V1*01', 'V1*02', 'V1*03'])
merge_def2 = EventMergeDefinition('V2')
merge_def2.extend(['V2*01'])
merge_defs = DistributionEventMergeDefinitions(
'v_gene',
bayesian_network_1,
allow_unspecified_events=True,
assert_merge_definitions=True)
with pytest.raises(ValueError) as e:
merge_defs.set_merge_definitions([merge_def1, merge_def2])
assert str(
e.value
) == DistributionEventMergeDefinitions.ERR_ONLY_ONE_MERGE_DEF_ALLOWED_MSG
def test_marginals_7__merge_all_alleles(bayesian_network_3):
wrapper = BayesianNetworkWrapper(bayesian_network_3)
merge_def1 = EventMergeDefinition('V1')
merge_def1.extend(['V1*01', 'V1*02'])
merge_defs = DistributionEventMergeDefinitions(
'v_gene',
wrapper.get_network(),
allow_unspecified_events=True,
assert_merge_definitions=True)
merge_defs.set_merge_definitions([merge_def1])
merged_network = wrapper.create_network_with_merged_events(merge_defs)
assert (merged_network is not None)
wrapper = BayesianNetworkWrapper(merged_network)
margs = wrapper.get_probabilities(
statename=None, probability_type=ProbabilityType.Conditional)
assert len(margs) == 7
def test_marginals_5__merge_v_alleles(bayesian_network_1):
wrapper = BayesianNetworkWrapper(bayesian_network_1)
merge_def1 = EventMergeDefinition('V1')
merge_def1.extend(['V1*01', 'V1*02', 'V1*03'])
merge_defs = DistributionEventMergeDefinitions(
'v_gene',
bayesian_network_1,
allow_unspecified_events=True,
assert_merge_definitions=True)
merge_defs.set_merge_definitions([merge_def1])
merged_network = wrapper.create_network_with_merged_events(merge_defs)
wrapper = BayesianNetworkWrapper(merged_network)
margs = wrapper.get_probabilities(
statename='v_gene', probability_type=ProbabilityType.Conditional)
assert len(margs) == 2
assert utilities.almost_equal(margs.iloc[0, 0], 0.6, 0.0001)
assert utilities.almost_equal(margs.iloc[1, 0], 0.4, 0.0001)
def test_marginals_4__merge_v_alleles(bayesian_network_1):
wrapper = BayesianNetworkWrapper(bayesian_network_1)
merge_def1 = EventMergeDefinition('V1')
merge_def1.extend(['V1*01', 'V1*02', 'V1*03'])
merge_defs = DistributionEventMergeDefinitions(
'v_gene',
bayesian_network_1,
allow_unspecified_events=True,
assert_merge_definitions=True)
merge_defs.set_merge_definitions([merge_def1])
merged_network = wrapper.create_network_with_merged_events(merge_defs)
wrapper = BayesianNetworkWrapper(merged_network)
margs = wrapper.get_probabilities(
statename=None, probability_type=ProbabilityType.Marginal)
assert len(margs) == 2
for key, value in margs.iteritems():
tot = value.sum()
assert utilities.almost_equal(tot, 1.0, 0.0001)
def test_merge_definitions_6__events_not_unique(bayesian_network_0):
merge_def1 = EventMergeDefinition('V1')
merge_def1.extend(['V1*01', 'V1*02', 'V1*03'])
with pytest.raises(ValueError) as e:
merge_defs = DistributionEventMergeDefinitions(
'v_gene',
bayesian_network_0,
allow_unspecified_events=True,
assert_merge_definitions=True)
assert str(
e.value
) == DistributionEventMergeDefinitions.ERR_NETWORK_HAS_DUPLICATED_EVENT_NAMES