getPatientInfo.py

def interpretPy(kind, value):
    if "NA": return None
    answer = {"SEX": {True: "Male", False: "Female"},
            "VITAL_STATUS": {True: "ALIVE", False: "DECEASED"},
            "SMOKING_HISTORY": {1: "Prev/Curr Smoker", 0: "Never", -1: "Unknown"},
            "OS_STATUS": {True: "LIVING", False: "DECEASED"}}
    return answer[kind][value]

def interpretMan(kind, value):
    if None: return "NA"
    answer = {"SEX": {"Male": True, "Female": False},
            "VITAL_STATUS": {"ALIVE": True, "DECEASED": False},
            "SMOKING_HISTORY": {"Prev/Curr Smoker": 1, "Never": 0, "Unknown": -1},
            "OS_STATUS": {"LIVING": True, "DECEASED": False}}
    return answer[kind][value]

def selectPatient(patient, kind, value):
    value = interpretMan(kind, value)
    names = list(patient.keys())
    
    for name in names:
        if patient[name][kind] != value:
            del(patient[name])
    return patient

def getPatientInfo(fileName, review=True):
    patient = dict()
    infomations = list()
    infomationsFile = open(fileName, "r")

    for _ in range(4): assert infomationsFile.readline()

    infomations = infomationsFile.readline().split()
    
    while True:
        line = infomationsFile.readline()
        if not line: break
        line = line.strip().split("\t")
        
        name = None
        for i, val_i in enumerate(line):
            if i == 0:
                assert val_i not in patient
                patient[val_i] = dict()
                name = val_i
            elif i == 1:
                if val_i == "Male": patient[name][infomations[i]] = True
                elif val_i == "Female": patient[name][infomations[i]] = False
                else: raise WrongSexInfo
            elif i == 2 or i == 5:
                if val_i == "ALIVE" or val_i == "LIVING": patient[name][infomations[i]] = True
                elif val_i == "DECEASED": patient[name][infomations[i]] = False
                elif val_i == "NA": patient[name][infomations[i]] = val_i
                else: raise WrongAliveInfo
            elif i == 3:
                if val_i == "Prev/Curr Smoker": patient[name][infomations[i]] = 1
                elif val_i == "Never": patient[name][infomations[i]] = 0
                elif val_i == "Unknown": patient[name][infomations[i]] = -1
                elif val_i == "NA": patient[name][infomations[i]] = val_i
                else: raise WrongSmokingInfo
            elif i == 4:
                if val_i == "NA": patient[name][infomations[i]] = val_i
                else: patient[name][infomations[i]] = float(val_i)
            else: raise WrongInfo
    infomationsFile.close()
    return patient

if __name__ == "__main__":
    info = getPatientInfo("../msk_impact_2017/data_clinical_patient.txt")
    print(len(info))
    info = selectPatient(info, "SMOKING_HISTORY", "Never")
    print(len(info))