def create_merge_definition_list(gen_model_event,
prefix=None,
merge_singleton_events=False):
genes = ir_genes.Genes()
for realization in gen_model_event.realizations:
r_name = realization.name.strip()
gene = ir_gene.Gene(r_name, assume_01_allele=False)
if len(gene.get_allele_text()) < 1:
raise ValueError('Gene name does not contain allele')
genes.add_gene(gene)
unique_genes = {}
for gene in genes:
gene_def = gene.get_gene_text()
unique_gene = unique_genes.get(gene_def, None)
if unique_gene is None:
unique_gene = ir_genes.GenePossibilities()
unique_genes[gene_def] = unique_gene
unique_gene.add_gene(gene, also_check_allele=True)
merge_defs = []
for gene_def, unique_gene in unique_genes.iteritems():
# Singleton events (genes with one allele only) do not have to be merged; this is optional
if len(unique_gene) > 1 or merge_singleton_events:
merged_event_name = gene_def
if prefix is not None:
merged_event_name = prefix + merged_event_name
merge_def = EventMergeDefinition(merged_event_name)
for g in unique_gene:
if prefix: s = prefix
s += str(g)
merge_def.add(s)
merge_defs.append(merge_def)
return merge_defs
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
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_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_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