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

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author bimib
date Wed, 06 Nov 2024 13:57:24 +0000
parents 726e1dc71f03
children 00a66b9bc29e
comparison
equal deleted inserted replaced
146:88cf4543e210 147:3fca9b568faf
8 import sys 8 import sys
9 import csv 9 import csv
10 from joblib import Parallel, delayed, cpu_count 10 from joblib import Parallel, delayed, cpu_count
11 11
12 ################################# process args ############################### 12 ################################# process args ###############################
13 def process_args(args :List[str]) -> argparse.Namespace: 13 def process_args(args :List[str] = None) -> argparse.Namespace:
14 """ 14 """
15 Processes command-line arguments. 15 Processes command-line arguments.
16 16
17 Args: 17 Args:
18 args (list): List of command-line arguments. 18 args (list): List of command-line arguments.
64 help = 'ras selector') 64 help = 'ras selector')
65 65
66 parser.add_argument('-cc', '--cell_class', 66 parser.add_argument('-cc', '--cell_class',
67 type = str, 67 type = str,
68 help = 'output of cell class') 68 help = 'output of cell class')
69 69 parser.add_argument(
70 70 '-idop', '--output_path',
71 ARGS = parser.parse_args() 71 type = str,
72 default='ras_to_bounds/',
73 help = 'output path for maps')
74
75
76 ARGS = parser.parse_args(args)
72 return ARGS 77 return ARGS
73 78
74 ########################### warning ########################################### 79 ########################### warning ###########################################
75 def warning(s :str) -> None: 80 def warning(s :str) -> None:
76 """ 81 """
199 pass 204 pass
200 205
201 206
202 207
203 ############################# main ########################################### 208 ############################# main ###########################################
204 def main() -> None: 209 def main(args:List[str] = None) -> None:
205 """ 210 """
206 Initializes everything and sets the program in motion based on the fronted input arguments. 211 Initializes everything and sets the program in motion based on the fronted input arguments.
207 212
208 Returns: 213 Returns:
209 None 214 None
211 if not os.path.exists('ras_to_bounds'): 216 if not os.path.exists('ras_to_bounds'):
212 os.makedirs('ras_to_bounds') 217 os.makedirs('ras_to_bounds')
213 218
214 219
215 global ARGS 220 global ARGS
216 ARGS = process_args(sys.argv) 221 ARGS = process_args(args)
217
218 ARGS.output_folder = 'ras_to_bounds/'
219 222
220 if(ARGS.ras_selector == True): 223 if(ARGS.ras_selector == True):
221 ras_file_list = ARGS.input_ras.split(",") 224 ras_file_list = ARGS.input_ras.split(",")
222 ras_file_names = ARGS.name.split(",") 225 ras_file_names = ARGS.name.split(",")
223 if len(ras_file_names) != len(set(ras_file_names)): 226 if len(ras_file_names) != len(set(ras_file_names)):
267 ARGS.medium_selector = ARGS.medium_selector.replace("_", " ") 270 ARGS.medium_selector = ARGS.medium_selector.replace("_", " ")
268 medium = df_mediums[[ARGS.medium_selector]] 271 medium = df_mediums[[ARGS.medium_selector]]
269 medium = medium[ARGS.medium_selector].to_dict() 272 medium = medium[ARGS.medium_selector].to_dict()
270 273
271 if(ARGS.ras_selector == True): 274 if(ARGS.ras_selector == True):
272 generate_bounds(model, medium, ras = ras_combined, output_folder=ARGS.output_folder) 275 generate_bounds(model, medium, ras = ras_combined, output_folder=ARGS.output_path)
273 class_assignments.to_csv(ARGS.cell_class, sep = '\t', index = False) 276 class_assignments.to_csv(ARGS.cell_class, sep = '\t', index = False)
274 else: 277 else:
275 generate_bounds(model, medium, output_folder=ARGS.output_folder) 278 generate_bounds(model, medium, output_folder=ARGS.output_path)
276 279
277 pass 280 pass
278 281
279 ############################################################################## 282 ##############################################################################
280 if __name__ == "__main__": 283 if __name__ == "__main__":