changeset 213:e078bc425eca draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/marea_2_0/model_generator.py	Fri Jul 05 16:15:18 2024 +0000
@@ -0,0 +1,100 @@
+import argparse
+import utils.general_utils as utils
+from typing import Optional, List
+import os
+import numpy as np
+import pandas as pd
+import cobra
+from joblib import Parallel, delayed, cpu_count
+import sys
+
+################################# process args ###############################
+def process_args(args :List[str]) -> argparse.Namespace:
+    """
+    Processes command-line arguments.
+
+    Args:
+        args (list): List of command-line arguments.
+
+    Returns:
+        Namespace: An object containing parsed arguments.
+    """
+    parser = argparse.ArgumentParser(usage = '%(prog)s [options]',
+                                     description = 'process some value\'s')
+
+    parser.add_argument('-ol', '--out_log', 
+                        help = "Output log")
+    
+    parser.add_argument('-td', '--tool_dir',
+                        type = str,
+                        required = True,
+                        help = 'your tool directory')
+    
+    
+    parser.add_argument('-im', '--input_medium',
+                        required = True,
+                        type=str,
+                        help = 'input medium')
+    
+    parser.add_argument('-ir', '--input_ras',
+                        required = True,
+                        type=str,
+                        help = 'input ras')
+    
+    parser.add_argument('-ot', '--output_type', 
+                        type = str,
+                        required = True,
+                        help = 'output type')
+    
+    ARGS = parser.parse_args()
+    return ARGS
+
+########################### warning ###########################################
+def warning(s :str) -> None:
+    """
+    Log a warning message to an output log file and print it to the console.
+
+    Args:
+        s (str): The warning message to be logged and printed.
+    
+    Returns:
+      None
+    """
+    with open(ARGS.out_log, 'a') as log:
+        log.write(s + "\n\n")
+    print(s)
+
+
+def write_to_file(dataset: pd.DataFrame, name: str, keep_index:bool=False)->None:
+    dataset.to_csv(ARGS.output_folder + name + ".csv", sep = '\t', index = keep_index)
+
+
+############################# main ###########################################
+def main() -> None:
+    """
+    Initializes everything and sets the program in motion based on the fronted input arguments.
+
+    Returns:
+        None
+    """
+    if not os.path.exists('model_generator'):
+        os.makedirs('model_generator')
+
+    num_processors = cpu_count()
+
+    global ARGS
+    ARGS = process_args(sys.argv)
+
+    ARGS.output_folder = 'model_generator/'
+    
+    
+    ras_inputs = ARGS.input_ras.split(",")
+    ARGS.output_types = ARGS.output_type.split(",")
+
+    ras = pd.read_table(ras_inputs[0], header=0, sep=r'\s+', index_col = 0)
+
+    pass
+        
+##############################################################################
+if __name__ == "__main__":
+    main()
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