항생제 TFT 연구 #1 입력 데이터 생성 #

%load_ext autoreload
%autoreload 2

import sys
import os

sys.path.append('/data3/projects/2025_Antibiotics/YSH/bin')
from sc import *

os.chdir('/data3/projects/2025_Antibiotics/YSH')

raw_path = '/data3/projects/2025_Antibiotics/YSH/res/sev_dict_filtered.pkl'

with open(raw_path, 'rb') as f:
    raw_data = pickle.load(f)

keys = list(raw_data.keys())
print(len(keys))
print(keys[0], '\n', raw_data[keys[0]])

4515
74374 
         Date  NEWS  med_cnt                    med_list  \
0 2020-10-30     4        2          Trizele;Cefotaxime   
1 2020-10-31     4        2          Trizele;Cefotaxime   
2 2020-11-01    12        2         Pospenem;Pospenem_2   
3 2020-11-02     9        3  Pospenem;Meropen;Vanco Kit   
4 2020-11-03    12        2           Vanco Kit;Meropen   
5 2020-11-04     8        2           Vanco Kit;Meropen   
6 2020-11-05     9        0                               

                               strain  
0                                  []  
1                                  []  
2                                  []  
3  [Enterobacter cloacae ssp cloacae]  
4  [Enterobacter cloacae ssp cloacae]  
5  [Enterobacter cloacae ssp cloacae]  
6  [Enterobacter cloacae ssp cloacae]  

indir = 'res'

with open(f"{indir}/all_meds.txt", 'r') as f:
    all_meds = [line.strip() for line in f if line.strip()]
    all_meds = [s.replace("/", "_") for s in all_meds]

print(len(all_meds))
print(all_meds)

169
['Sevatrim', 'Nystatin syrup', 'Fungizone', 'Vancozin', 'Gavir', 'Regkirona', 'Omnicef Granule_g', 'Pyrazinamide', 'Cotrim', 'Ubacsin', 'Netilmicin', 'Cycin', 'Amoxicle', 'Vancomycin HCl', 'Anycef', 'Valcyte', 'Septrin tab', 'Imicil Kit', 'Rifampin', 'Enped', 'Meropen', 'Valvirus', 'Azitops', 'Viramid', 'Cymevene', 'Flumarin', 'Yuhanzid', 'Foxolin', 'Vgavir', 'Suprax', 'Vivir', 'Cefetat', 'Pospenem', 'Minocin', 'Ceftazidime', 'Banan dry syrup', 'Vivaquine', 'Rifodex', 'Duricef', 'Tygacil', 'Amocla duo tab', 'Famvics', 'Baraclude', 'Veklury', 'Taurolin', 'Diflucan POS', 'Rulid', 'Klaricid Dry syrup', 'Teracycline', 'Closerin', 'Zithromax Dry Syrup', 'Tapocin', 'Zinperazone', 'Amoxapen', 'Prevymis', 'Trison Kit', 'Aclova', 'Doxycyclin', 'Cefazedone', 'Finipenem', 'Cefazolin', 'Epocelin', 'Ceftezole', 'Ciprobay', 'Adefovir', 'Tamiflu', 'Zavicefta', 'Nafcillin Sodium', 'Bearcef', 'Linoped', 'Prepenem', 'Roxithromycin', 'Cravit', 'Invanz', 'Tobra', 'Zeffix', 'Sporanox cap', 'Ampibactam', 'Levoplus', 'Itra', 'Cravit tab', 'Viread', 'Zithromax', 'Penbrex', 'Paxlovid', 'Myambutol', 'Daptocin', 'Finibax', 'Zyvox', 'Omnicef', 'Colis', 'Amoxicillin', 'Flasinyl', 'Pentamidine Isethionate', 'Kaletra', 'Adikan', 'Maxipime', 'Amikacin', 'Triaxone', 'Ceradolan', 'Moveloxin', 'Meiact', 'Hanmiflu solution', 'Avelox', 'Acillin', 'Entecabell ODT', 'Fullgram', 'Ceftil', 'Augmentin', 'Remdesivir', 'Lagevrio', 'Lamiffix', 'Ambisome', 'Monodoxy-M', 'Unasyn', 'Prezcobix', 'Ceftriaxone', 'Noxafil tab', 'Tiroxin', 'Rukasyn', 'Amikin', 'Prothionamide', 'Gentamicin', 'Hanomycin', 'Monurol', 'Mezactam', 'Plunazol', 'Cancidas', 'Citopcin', 'Claric', 'Isepacin', 'Oxiklorine', 'Nitrofurantoin', 'Combicin', 'Mycamine', 'Amocla Duo Syrup', 'Distocide', 'Rulid D', 'Meicelin', 'Tazocin', 'Vfend', 'Zerbaxa', 'Akocin', 'Yamatetan', 'Oneflu', 'Sebivo', 'Enteone', 'Trizele', 'Gomcephin', 'Amocla', 'Banan Dry Syrup', 'Synagis', 'Isepamicin', 'Famvir', 'Dexamethasone Inj', 'Sporanox Oral Solution', 'Pamoxin Dry Syrup', 'Vanco Kit', 'Factive', 'Cefotaxime', 'Casfun', 'Banan', 'Tubes', 'Eraxis', 'Ubacillin', 'Dexamethasone', 'Normix', 'Peramiflu', 'Vemlidy']

indir = 'res'
outdir = 'data/sev_dict'

for med in all_meds:
    print(med)
    sev_dict = make_sev_dict(med, indir, outdir)

#1
indir = 'data/sev_dict'
outdir = 'data/timecourse'

for med in all_meds:
    timecourse = make_timecourse(indir, outdir, med)

#2
indir = 'data/timecourse'
outdir = 'data/sev_idx'

for med in all_meds:
    sev_idx = make_sev_idx(indir, outdir, med)

#3
indir = 'data/sev_dict'
indexdir = 'data/sev_idx'
outdir = 'data/res_dict'

for med in all_meds:
    res_dict = make_res_dict(indir, indexdir, outdir, med)

cur_path = 'data/res_dict'
cur_med = 'Dexamethasone'

with open(f"{cur_path}/{cur_med}", 'rb') as f:
    res_dict = pickle.load(f)

cur_keys = list(res_dict.keys())
print(len(cur_keys))
print(res_dict[cur_keys[0]])

783
         Date  NEWS  med_cnt                        strain
4  2017-08-18     4        0  [Staphylococcus epidermidis]
5  2017-08-19     4        0  [Staphylococcus epidermidis]
6  2017-08-20     4        0  [Staphylococcus epidermidis]
7  2017-08-21     4        1  [Staphylococcus epidermidis]
8  2017-08-22     3        1  [Staphylococcus epidermidis]
9  2017-08-23     4        1  [Staphylococcus epidermidis]
10 2017-08-24     4        1      [Pseudomonas aeruginosa]
11 2017-08-25     7        1      [Pseudomonas aeruginosa]
12 2017-08-26     4        1      [Pseudomonas aeruginosa]
13 2017-08-27     4        1      [Pseudomonas aeruginosa]