def __init__(self, source, EXP_ID, exp_id, n_same_time=None): if n_same_time: fl = './_data/patients/'\ +source+'_patients_disease_'+n_same_time+'.pkl' else: fl = './_data/patients/' + source + '_patients_disease.pkl' fn = './_data/results/sims/'\ +source+'_patient_sims_'+EXP_ID+'_'+exp_id+'.pkl' self.patient_similarities = load_object(fn) self.patients_disease = load_object(fl) self.y = [] self.sim_names = { 'cos_sim', 'jaccard_best_avg', 'resnik_best_avg', 'lin_best_avg', 'jc_best_avg' } self.fpr = {} self.tpr = {} self.thresholds = {} self.roc_auc = {} self.cos_sim = [] self.jaccard_best_avg = [] self.resnik_best_avg = [] self.lin_best_avg = [] self.jc_best_avg = [] self.x = len(self.patient_similarities) self.z = self.x - 1 """ Why is m = x*z / 2 instead of z*z/2 ?????? """ self.m = self.x * self.z / 2 self.get_results()
def __load_pkl(self, filename_pkl): db = load_object(filename_pkl) self.decipher = db['decipher'] self.decipher_desc = db['decipher_desc'] self.orpha = db['orpha'] self.orpha_desc = db['orpha_desc'] self.omim = db['omim'] self.omim_desc = db['omim_desc']
def __init__(self, source, EXP_ID, exp_id, n_same_time=None): if n_same_time: fl = './_data/patients/'\ +source+'_patients_disease_'+n_same_time+'.pkl' else: fl = './_data/patients/'+source+'_patients_disease.pkl' fn = './_data/results/sims/'\ +source+'_patient_sims_'+EXP_ID+'_'+exp_id+'.pkl' self.patient_similarities = load_object(fn) self.patients_disease = load_object(fl) self.cos_sim = [] self.jaccard_best_avg = [] self.resnik_best_avg = [] self.lin_best_avg = [] self.jc_best_avg = [] self.build_patient_sim_matrix()
def __init__(self, fn='_data/hpo/hp.obo'): ext = fn[-4:].lower() if ext == '.obo': self.hpos = self.__parse(fn) self.__build_children(self.hpos) elif ext == '.pkl': self.hpos = load_object(fn) else: raise ValueError( 'Invalid file extension: Expected .obo or .pkl, found {}'. format(ext))
def load_pkl(self, fn): db = load_object(fn) self.decipher = db['decipher'] self.orpha = db['orpha'] self.omim = db['omim']
def __load_pkl(self, fn_pkl): db = load_object(fn_pkl) self.name2id = db['name2id'] self.id2name = db['id2name'] self.id2desc = db['id2desc']