encoding="utf-8",
delay=0)
my_handler.setFormatter(
logging.Formatter('%(asctime)s %(levelname)s %(message)s'))
my_handler.setLevel(logging.INFO)
logger = logging.getLogger("OKP")
logger.setLevel(logging.INFO)
logger.addHandler(my_handler)
logger.info(
"===================== Started a new session =====================")
# Load the config file and start the connection
config = configparser.ConfigParser()
config.read('EKP/config.ini')
# Set up the connection
c = connection(config)
#TODO: Filter implementeren voor indirect verbonden eiwitten
# Load the drug targets by UNIPROT ID and RXNORM ID, keep only the ones which have more than 5 targets
nature = open("EKP/Roche/Input/Nature_Targets.csv", "r")
csv_reader = csv.reader(nature)
next(csv_reader)
target_dict = {}
for l in csv_reader:
if l[10] is not '' and l[4] is not '':
try:
protID = c.getID(l[4],
"Amino Acid, Peptide, or Protein",
knowledgebase="uniprot")['content']
if len(protID) == 1:
if l[10] not in target_dict.keys():
# Load the connection
from EKP.EKP2 import connection
import os
import csv
import configparser
import logging
os.chdir('/Users/Wytze/git/ODEX4all-UseCases/EKP')
logging.basicConfig(filename='logs/Roche.log',level=logging.DEBUG)
logging.info("===================== Started a new session =====================")
config = configparser.ConfigParser()
config.read('config.ini')
# Set up the connection
c = connection(config)
# Read in the targets of the drugs
target_dict = {}
input = open("Roche/drug_target_uniprot_links.csv", "r")
reader = csv.reader(input, delimiter = ",")
for line in reader:
if line[0] not in target_dict.keys():
target_dict[line[0]] = [line[3]]
else:
target_dict[line[0]].append(line[3])
input.close()
# Load the data
input = open("Roche/DiseaseTarget_referenceSet.csv", "r")
reader = csv.reader(input, delimiter = ";")
reader.__next__()