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']