def main(argv):
u = Utils()
iterations = 25
idx = int(argv[1])
drugs = u.load_np('drugs')
drugID = drugs[idx]
status = u.read_status(drugID)
if status == 'no':
try:
u.write_status(drugID, 'working')
drug = Drug(drugID)
for itr in range(1, iterations + 1):
drug.match()
drug.count_adr()
drug.assign_abcd(itr)
drug.do_chi_square()
drug.calc_logROR()
drug.reset_for_next_itr()
x = drug.save_results(iterations)
if x:
u.write_status(drugID, 'yes')
else:
u.write_status(drugID, 'no')
except:
info = str(sys.exc_info()[1])
u.write_status(drugID, 'error ' + info)
def main(argv):
i = int(argv[1])
u = Utils()
db = Database('Mimir from Munnin')
np.random.seed(u.RANDOM_STATE)
df_patients = u.load_df('df_patients')
sex_adr = db.get_list('select meddra_pt_id from gender_terms')
drugs = db.get_list('select atc_5_id from atc_5_name')
test = [(x, y) for x, y in u.load_np('prr_test')]
df_test = pd.DataFrame(test, columns=['drug',
'adr']).sort_values(by='drug')[i:]
PID_M = set(df_patients.query('Sex=="M"').get('PID').values)
PID_F = set(df_patients.query('Sex=="F"').get('PID').values)
for drugID, data in df_test.groupby('drug'):
filename = 'Post_PRR/' + str(drugID)
pth = u.DATA_PATH + filename + '.feather'
if os.path.exists(pth):
print(drugID)
continue
prr_counts = []
q = 'select PID from atc_5_patient where atc_5_id = ' + str(drugID)
takes_drug = set(db.get_list(q))
try:
drug = Drug(drugID)
drug.match()
except NameError:
df = pd.DataFrame(
columns=['drug', 'adr', 'sex', 'a_post', 'c_post'])
u.save_df(df, filename)
if drug.match_m is None or drug.match_f is None:
df = pd.DataFrame(
columns=['drug', 'adr', 'sex', 'a_post', 'c_post'])
u.save_df(df, filename)
db = Database('Mimir from Munnin')
continue
for adrID in data.adr.values:
q = 'select PID from pt_patient where meddra_concept_id = ' + str(
adrID)
has_adr = set(db.get_list(q))
for sex in ['M', 'F']:
if sex == 'M': PSM = drug.match_m
else: PSM = drug.match_f
a_post = len([1 for x in PSM if x in (has_adr & takes_drug)])
c_post = len([1 for x in PSM if x in (takes_drug - has_adr)])
res = {
'drug': drugID,
'adr': adrID,
'sex': sex,
'a_post': a_post,
'c_post': c_post
}
prr_counts.append(res)
df = pd.DataFrame(prr_counts)
u.save_df(df, filename)
break
