def processPathwayBKF(self, exhaustiveOr=False):
assert len(self.pathways) > 0, "Have not processed pathways yet"
for pathway in tqdm.tqdm(self.pathways,
desc='Processing pathway BKFs'):
bkf = BKB(name=pathway.pathwayID)
pathwayActiveComp_idx = bkf.addComponent('{}_active='.format(
pathway.pathwayID))
pathwayActiveTrue_idx = bkf.addComponentState(
pathwayActiveComp_idx, 'True')
if exhaustiveOr:
print("not implemented")
else:
geneSelectorComp_idx = bkf.addComponent("Gene_combo=")
for gene in pathway.genes: #gene[0] = geneName, gene[1] = low value gene[2] = high value
geneCombo_idx = bkf.addComponentState(
geneSelectorComp_idx, gene[0])
statConditionComp_idx = bkf.addComponent(
'mu-STD<={}<=mu+STD='.format(gene[0]))
statConditionTrue_idx = bkf.addComponentState(
statConditionComp_idx, 'True')
bkf.addSNode(
BKB_S_node(statConditionComp_idx,
statConditionTrue_idx, 1.0))
bkf.addSNode(
BKB_S_node(
geneSelectorComp_idx, geneCombo_idx, 1.0,
[(statConditionComp_idx, statConditionTrue_idx)]))
bkf.addSNode(
BKB_S_node(pathwayActiveComp_idx,
pathwayActiveTrue_idx, 1.0,
[(geneSelectorComp_idx, geneCombo_idx)]))
self.bkfs.append(bkf)
assert len(self.pathways) > 0, "Have not processed pathways yet"
for gene2 in GENES:
count = 0
for patient in PATIENTS:
if patient_data[patient]['Genes'][gene1] and patient_data[patient][
'Genes'][gene2]:
count += 1
counts[(gene1, gene2)] = float(count / len(PATIENTS)) / priors[gene2]
#-- Make BKB Patient frags
for patient in PATIENTS:
bkf = BKB()
for gene in patient_data[patient]['Genes']:
#-- Setup Gene i component.
geneComp_idx = bkf.addComponent(gene)
geneStateTrue_idx = bkf.addComponentState(geneComp_idx, 'True')
s_node_prior = BKB_S_node(init_component_index=geneComp_idx,
init_state_index=geneStateTrue_idx,
init_probability=1)
bkf.addSNode(s_node_prior)
patient_bkfs.append(bkf)
#-- Define Sample Pathway
PATHWAYS = ['Pathway{}'.format(i) for i in range(1)]
pathway_data = {
pathway: {
gene: random.random() / 10
for gene in set([random.choice(GENES) for _ in range(len(GENES))])
}
'Age': random.randrange(AGE_RANGE_YRS[0], AGE_RANGE_YRS[1]),
'Survival': random.randrange(SURIVAL_YRS[0], SURIVAL_YRS[1])
}
for patient in PATIENTS
}
bkfs = list()
#-- Make BKB frags
for patient in PATIENTS:
bkf = BKB()
for gene in GENES:
if random.choice([True, False]):
#-- Setup Gene i component.
comp_idx = bkf.addComponent('mut_{}'.format(gene))
stateTrue_idx = bkf.addComponentState(comp_idx, 'True')
bkf.addSNode(
BKB_S_node(init_component_index=comp_idx,
init_state_index=stateTrue_idx,
init_probability=1))
variant_comp_idx = bkf.addComponent('mut-var_{}'.format(gene))
random_variant = random.choice(GENE_VARIANTS)
variant_state_idx = bkf.addComponentState(variant_comp_idx,
random_variant)
bkf.addSNode(
BKB_S_node(init_component_index=variant_comp_idx,
init_state_index=variant_state_idx,
init_probability=1,
init_tail=[(comp_idx, stateTrue_idx)]))
if 'Patient_Genes' not in patient_data[patient]:
def processPathwayBKF(self, exhaustiveOr=False):
assert len(self.pathways) > 0, "Have not processed pathways yet"
for pathway in tqdm.tqdm(self.pathways,
desc='Processing pathway BKFs'):
bkf = BKB(name=pathway.ID)
if "_hier" in pathway.ID:
#head
pathwayParentComp_idx = bkf.addComponent('{}_active='.format(
pathway.head))
pathwayParentTrue_idx = bkf.addComponentState(
pathwayParentComp_idx, 'True')
#tail - should only be 1 for _hier bkfs
pathwayChildComp_idx = bkf.addComponent('{}_active='.format(
pathway.tails[0]))
pathwayChildTrue_idx = bkf.addComponentState(
pathwayChildComp_idx, 'True')
#S-node
bkf.addSNode(
BKB_S_node(pathwayChildComp_idx, pathwayChildTrue_idx,
1.0))
bkf.addSNode(
BKB_S_node(pathwayParentComp_idx, pathwayParentTrue_idx,
1.0,
[(pathwayChildComp_idx, pathwayChildTrue_idx)]))
else:
'''
#head
pathwayHierComp_idx = bkf.addComponent('{}_active='.format(pathway.head))
pathwayHierTrue_idx = bkf.addComponentState(pathwayHierComp_idx, 'True')
#tails
for tail in pathway.tails:
statConditionComp_idx = bkf.addComponent('mu-STD<={}<=mu+STD'.format(tail))
statConditionTrue_idx = bkf.addComponentState(statConditionComp_idx, 'True')
bkf.addSNode(BKB_S_node(statConditionComp_idx, statConditionTrue_idx, 1.0))
bkf.addSNode(BKB_S_node(pathwayHierComp_idx, pathwayHierTrue_idx, 1.0, [(statConditionComp_idx, statConditionTrue_idx)]))
self.bkfs.append(bkf)
'''
#=======
if exhaustiveOr:
print("not implemented")
else:
# pathway
pathwayReactionComp_idx = bkf.addComponent(pathway.head +
"_active=")
pathwayReactionTrue_idx = bkf.addComponentState(
pathwayReactionComp_idx, 'True')
# gene slector
geneSelectorComp_idx = bkf.addComponent("Gene_combo=")
#tails
for tail in pathway.tails:
geneCombo_idx = bkf.addComponentState(
geneSelectorComp_idx, tail)
statConditionComp = BKB_component("mu-STD>=" + tail +
"<=mu+STD=")
statConditionTrue = BKB_I_node('True',
statConditionComp)
statConditionComp_idx = bkf.addComponent("mu-STD>=" +
tail +
"<=mu+STD=")
statConditionTrue_idx = bkf.addComponentState(
statConditionComp_idx, 'True')
bkf.addSNode(
BKB_S_node(statConditionComp_idx,
statConditionTrue_idx, 1.0))
bkf.addSNode(
BKB_S_node(geneSelectorComp_idx, geneCombo_idx,
1.0, [(statConditionComp_idx,
statConditionTrue_idx)]))
bkf.addSNode(
BKB_S_node(
pathwayReactionComp_idx,
pathwayReactionTrue_idx, 1.0,
[(geneSelectorComp_idx, geneCombo_idx)]))
self.bkfs.append(bkf)
def processPatientBKF(self):
assert len(
self.patients) > 0, "Have not processed Patient and gene data yet."
#print("Forming Patient BKFs...")
allGenes = list()
for pat in tqdm.tqdm(self.patients, desc='Forming patient BKFs'):
bkf = BKB(name=pat.patientID)
variantCompIndices = list()
variantCompNames = list()
variantCompStateIndices = list()
for idx, gene in enumerate(pat.mutatedGenes):
allGenes.append(gene)
# gene
mutGeneComp_idx = bkf.addComponent('mut_{}='.format(gene))
iNodeGeneMut_idx = bkf.addComponentState(
mutGeneComp_idx, 'True')
# form SNode o---->[mut_<genename>=True]
bkf.addSNode(BKB_S_node(mutGeneComp_idx, iNodeGeneMut_idx,
1.0))
if 'var_' + pat.variants[idx] + '=' in variantCompNames:
cIdx = variantCompNames.index('var_{}='.format(
pat.variants[idx]))
#mut_var combo
mutVarComp_idx = bkf.addComponent('mut-var_{}='.format(
pat.mutatedGeneVariants[idx]))
iNodeMutVar_idx = bkf.addComponentState(
mutVarComp_idx, 'True')
#mut_var s-node
bkf.addSNode(
BKB_S_node(mutVarComp_idx, iNodeMutVar_idx, 1.0,
[(mutGeneComp_idx, iNodeGeneMut_idx),
(variantCompIndices[cIdx],
variantCompStateIndices[cIdx])]))
else:
#var
variantComp_idx = bkf.addComponent('var_{}='.format(
pat.variants[idx]))
iNodeVariant_idx = bkf.addComponentState(
variantComp_idx, 'True')
#var s-node
bkf.addSNode(
BKB_S_node(variantComp_idx, iNodeVariant_idx, 1.0))
variantCompIndices.append(variantComp_idx)
variantCompStateIndices.append(iNodeGeneMut_idx)
variantCompNames.append(
bkf.getComponentName(variantComp_idx))
#mut_var combo
mutVarComp_idx = bkf.addComponent('mut-var_{}='.format(
pat.mutatedGeneVariants[idx]))
iNodeMutVar_idx = bkf.addComponentState(
mutVarComp_idx, 'True')
#mut_var s-node
bkf.addSNode(
BKB_S_node(mutVarComp_idx, iNodeMutVar_idx, 1.0,
[(mutGeneComp_idx, iNodeGeneMut_idx),
(variantComp_idx, iNodeVariant_idx)]))
self.bkfs.append(bkf)
from reasoner import Reasoner, _constructSNodesByHead
from query import Query
PATIENTS = ['Patient_{}'.format(i) for i in range(10)]
NUM_GENES = 5
bkfs = list()
#-- Make BKB frags
for j, _ in enumerate(PATIENTS):
bkf = BKB()
for i in range(NUM_GENES):
#-- Setup Gene i component.
comp_idx = bkf.addComponent('Gene{}_mutated'.format(i))
stateTrue_idx = bkf.addComponentState(comp_idx, 'True')
if random.choice([True, False]):
bkf.addSNode(
BKB_S_node(init_component_index=comp_idx,
init_state_index=stateTrue_idx,
init_probability=1))
bkfs.append(bkf)
#-- Fuse patients together.
fused_bkb = fuse(bkfs, [1 for _ in range(len(PATIENTS))],
[str(hash(patient)) for patient in PATIENTS],
working_dir=os.getcwd())
#-- Impose Structure while maintiaining mutual exclusivity.