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comparison COBRAxy/rps_generator.py @ 147:3fca9b568faf draft

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author bimib
date Wed, 06 Nov 2024 13:57:24 +0000
parents 41f35c2f0c7b
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146:88cf4543e210 147:3fca9b568faf
14 import utils.general_utils as utils 14 import utils.general_utils as utils
15 import utils.reaction_parsing as reactionUtils 15 import utils.reaction_parsing as reactionUtils
16 16
17 ########################## argparse ########################################## 17 ########################## argparse ##########################################
18 ARGS :argparse.Namespace 18 ARGS :argparse.Namespace
19 def process_args() -> argparse.Namespace: 19 def process_args(args:List[str] = None) -> argparse.Namespace:
20 """ 20 """
21 Processes command-line arguments. 21 Processes command-line arguments.
22 22
23 Args: 23 Args:
24 args (list): List of command-line arguments. 24 args (list): List of command-line arguments.
49 parser.add_argument('-rp', '--rps_output', 49 parser.add_argument('-rp', '--rps_output',
50 type = str, 50 type = str,
51 required = True, 51 required = True,
52 help = 'rps output') 52 help = 'rps output')
53 53
54 args = parser.parse_args() 54 args = parser.parse_args(args)
55 return args 55 return args
56 56
57 ############################ dataset name ##################################### 57 ############################ dataset name #####################################
58 def name_dataset(name_data :str, count :int) -> str: 58 def name_dataset(name_data :str, count :int) -> str:
59 """ 59 """
220 df = pd.DataFrame.from_dict(rps_scores) 220 df = pd.DataFrame.from_dict(rps_scores)
221 df.rename(columns={'Unnamed: 0': 'Reactions'}, inplace=True) 221 df.rename(columns={'Unnamed: 0': 'Reactions'}, inplace=True)
222 df.to_csv(ARGS.rps_output, sep = '\t', na_rep = "None", index = False) 222 df.to_csv(ARGS.rps_output, sep = '\t', na_rep = "None", index = False)
223 223
224 ############################ main #################################### 224 ############################ main ####################################
225 def main() -> None: 225 def main(args:List[str] = None) -> None:
226 """ 226 """
227 Initializes everything and sets the program in motion based on the fronted input arguments. 227 Initializes everything and sets the program in motion based on the fronted input arguments.
228 228
229 Returns: 229 Returns:
230 None 230 None
231 """ 231 """
232 global ARGS 232 global ARGS
233 ARGS = process_args() 233 ARGS = process_args(args)
234 234
235 # TODO:use utils functions vvv 235 # TODO:use utils functions vvv
236 with open(ARGS.tool_dir + '/local/pickle files/black_list.pickle', 'rb') as bl: 236 with open(ARGS.tool_dir + '/local/pickle files/black_list.pickle', 'rb') as bl:
237 black_list = pk.load(bl) 237 black_list = pk.load(bl)
238 238