compNames = fused_bkb.getAllComponentNames()
f = open(withheld_patients_file, 'r')
withheldPatientHashes = f.read().split(',')
patientDict = pickle.load(open(patient_data_file, 'rb'))
patientsMutationVariantEvidence = []
patientIDs = []
for withheldPatientHash in withheldPatientHashes:
withheldPatientDict = patientDict[int(withheldPatientHash)]
patientIDs.append(withheldPatientDict["Patient_ID"])
genes = withheldPatientDict["Patient_Genes"]
variants = withheldPatientDict["Patient_Variants"]
patientMutationVariantEvidence = dict()
for idx, mut in enumerate(genes[0:5]):
compName = 'mut-var_'+mut
if compName in compNames:
compIDX = fused_bkb.getComponentIndex(compName)
compStatesIDXs = fused_bkb.getAllComponentINodeIndices(compIDX)
stateNames = [fused_bkb.getComponentINodeName(compIDX,csIdx) for csIdx in compStatesIDXs]
if variants[idx] in stateNames:
patientMutationVariantEvidence[compName] = variants[idx]
patientsMutationVariantEvidence.append(patientMutationVariantEvidence)
target = ('Survival_Time', '<=', 943)
cross_validator = CrossValidator(fused_bkb,withheldPatientHashes, patient_data_file, patientDict)
cross_validator.run_demo_suite(target,
patientIDs,
patientsMutationVariantEvidence)
f = open(withheld_patients_file, 'r')
withheldPatientHashes = f.read().split(',')
patientDict = pickle.load(open(patient_data_file, 'rb'))
patientsMutationVariantEvidence = []
patientIDs = []
for withheldPatientHash in withheldPatientHashes:
withheldPatientDict = patientDict[int(withheldPatientHash)]
patientIDs.append(withheldPatientDict["Patient_ID"])
genes = withheldPatientDict["Patient_Genes"]
variants = withheldPatientDict["Patient_Variants"]
patientMutationVariantEvidence = dict()
for idx, mut in enumerate(genes[0:5]):
compName = 'mut-var_' + mut
if compName in compNames:
compIDX = fused_bkb.getComponentIndex(compName)
compStatesIDXs = fused_bkb.getAllComponentINodeIndices(compIDX)
stateNames = [
fused_bkb.getComponentINodeName(compIDX, csIdx)
for csIdx in compStatesIDXs
]
if variants[idx] in stateNames:
patientMutationVariantEvidence[compName] = variants[idx]
patientsMutationVariantEvidence.append(patientMutationVariantEvidence)
target = ('Survival_Time', '<=', 943)
cross_validator = CrossValidator(fused_bkb, withheldPatientHashes,
patient_data_file, patientDict)
cross_validator.run_demo_suite(target, patientIDs,
patientsMutationVariantEvidence)