changeset 225:5a2c9ec9525b draft

Uploaded

--- a/marea_2/flux_simulation.py	Sat Aug 03 08:49:49 2024 +0000
+++ b/marea_2/flux_simulation.py	Sat Aug 03 08:52:25 2024 +0000
@@ -31,17 +31,25 @@
                         type = str,
                         required = True,
                         help = 'your tool directory')
- 
-
+    
     parser.add_argument('-in', '--input',
                         required = True,
                         type=str,
-                        help = 'inputs model')
+                        help = 'inputs bounds')
     
-    parser.add_argument('-nm', '--name',
+    parser.add_argument('-ni', '--names',
                         required = True,
                         type=str,
-                        help = 'inputs model ids')
+                        help = 'cell names')
+ 
+    parser.add_argument(
+        '-ms', '--model_selector', 
+        type = utils.Model, default = utils.Model.ENGRO2, choices = [utils.Model.ENGRO2, utils.Model.Custom],
+        help = 'chose which type of model you want use')
+    
+    parser.add_argument("-mo", "--model", type = str)
+    
+    parser.add_argument("-mn", "--model_name", type = str, help = "custom mode name")
     
     parser.add_argument('-a', '--algorithm',
                         type = str,
@@ -100,7 +108,31 @@
 
 
 def write_to_file(dataset: pd.DataFrame, name: str, keep_index:bool=False)->None:
-    dataset.T.to_csv(ARGS.output_folder + name + ".csv", sep = '\t', index = keep_index)
+    dataset.to_csv(ARGS.output_folder + name + ".csv", sep = '\t', index = keep_index)
+
+############################ dataset input ####################################
+def read_dataset(data :str, name :str) -> pd.DataFrame:
+    """
+    Read a dataset from a CSV file and return it as a pandas DataFrame.
+
+    Args:
+        data (str): Path to the CSV file containing the dataset.
+        name (str): Name of the dataset, used in error messages.
+
+    Returns:
+        pandas.DataFrame: DataFrame containing the dataset.
+
+    Raises:
+        pd.errors.EmptyDataError: If the CSV file is empty.
+        sys.exit: If the CSV file has the wrong format, the execution is aborted.
+    """
+    try:
+        dataset = pd.read_csv(data, sep = '\t', header = 0, index_col=0, engine='python')
+    except pd.errors.EmptyDataError:
+        sys.exit('Execution aborted: wrong format of ' + name + '\n')
+    if len(dataset.columns) < 2:
+        sys.exit('Execution aborted: wrong format of ' + name + '\n')
+    return dataset
 
 
 
@@ -139,6 +171,7 @@
             ARGS.out_log)
             CBS_backend.randomObjectiveFunctionSampling_cobrapy(model, n_samples, df_coefficients.iloc[:,i*n_samples:(i+1)*n_samples], 
                                                     samples)
+        utils.logWarning(ARGS.output_folder +  model_name + '_'+ str(i)+'_CBS.csv', ARGS.out_log)
         samples.to_csv(ARGS.output_folder +  model_name + '_'+ str(i)+'_CBS.csv', index=False)
 
     samplesTotal = pd.DataFrame()
@@ -153,29 +186,42 @@
     pass
 
 
-def model_sampler(model_input:str, model_name:str)-> List[pd.DataFrame]:
-
-    model_type = utils.Model.Custom
-    model = model_type.getCOBRAmodel(customPath = utils.FilePath.fromStrPath(model_input), customExtension = utils.FilePath.fromStrPath(model_name).ext)
+def model_sampler(model_input_original:cobra.Model, bounds_path:str, cell_name:str)-> List[pd.DataFrame]:
 
-    utils.logWarning(
-        "Sampling model: " + model_name,
-        ARGS.out_log)
+    model_input = model_input_original.copy()
+    bounds_df = read_dataset(bounds_path, "bounds dataset")
+    for rxn_index, row in bounds_df.iterrows():
+        model_input.reactions.get_by_id(rxn_index).lower_bound = row.lower_bound
+        model_input.reactions.get_by_id(rxn_index).upper_bound = row.upper_bound
     
-    name = model_name.split('.')[0]
+    name = cell_name.split('.')[0]
     
     if ARGS.algorithm == 'OPTGP':
-        OPTGP_sampler(model, name, ARGS.n_samples, ARGS.thinning, ARGS.n_batches, ARGS.seed)
+        OPTGP_sampler(model_input, name, ARGS.n_samples, ARGS.thinning, ARGS.n_batches, ARGS.seed)
 
     elif ARGS.algorithm == 'CBS':
-        CBS_sampler(model,  name, ARGS.n_samples, ARGS.n_batches, ARGS.seed)
+        CBS_sampler(model_input,  name, ARGS.n_samples, ARGS.n_batches, ARGS.seed)
 
     df_mean, df_median, df_quantiles = fluxes_statistics(name, ARGS.output_types)
 
     if("fluxes" not in ARGS.output_types):
         os.remove(ARGS.output_folder  +  name + '.csv')
 
-    return df_mean, df_median, df_quantiles
+    returnList = []
+    returnList.append(df_mean)
+    returnList.append(df_median)
+    returnList.append(df_quantiles)
+
+    df_pFBA, df_FVA, df_sensitivity = fluxes_analysis(model_input, name, ARGS.output_type_analysis)
+
+    if("pFBA" in ARGS.output_type_analysis):
+        returnList.append(df_pFBA)
+    if("FVA" in ARGS.output_type_analysis):
+        returnList.append(df_FVA)
+    if("sensitivity" in ARGS.output_type_analysis):
+        returnList.append(df_sensitivity)
+
+    return returnList
 
 def fluxes_statistics(model_name: str,  output_types:List)-> List[pd.DataFrame]:
 
@@ -213,6 +259,47 @@
     
     return df_mean, df_median, df_quantiles
 
+def fluxes_analysis(model:cobra.Model,  model_name:str, output_types:List)-> List[pd.DataFrame]:
+
+    df_pFBA = pd.DataFrame()
+    
+    df_sensitivity= pd.DataFrame()
+
+    for output_type in output_types:
+        if(output_type == "pFBA"):
+            model.objective = "Biomass"
+            solution = cobra.flux_analysis.pfba(model)
+            fluxes = solution.fluxes
+            df_pFBA.loc[0,[rxn._id for rxn in model.reactions]] = fluxes.tolist()
+            df_pFBA = df_pFBA.reset_index(drop=True)
+            df_pFBA.index = [model_name]
+            df_pFBA = df_pFBA.astype(float).round(6)
+        elif(output_type == "FVA"):
+            fva = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8)
+            columns = []
+            for rxn in fva.index.to_list():
+                columns.append(rxn + "_min")
+                columns.append(rxn + "_max")
+            df_FVA= pd.DataFrame(columns = columns)
+            for index_rxn, row in fva.iterrows():
+                df_FVA.loc[0, index_rxn+ "_min"] = fva.loc[index_rxn, "minimum"]
+                df_FVA.loc[0, index_rxn+ "_max"] = fva.loc[index_rxn, "maximum"]
+            df_FVA = df_FVA.reset_index(drop=True)
+            df_FVA.index = [model_name]
+            df_FVA = df_FVA.astype(float).round(6)
+        elif(output_type == "sensitivity"):
+            model.objective = "Biomass"
+            solution_original = model.optimize().objective_value
+            reactions = model.reactions
+            single = cobra.flux_analysis.single_reaction_deletion(model)
+            newRow = []
+            df_sensitivity = pd.DataFrame(columns = [rxn.id for rxn in reactions], index = [model_name])
+            for rxn in reactions:
+                newRow.append(single.knockout[rxn.id].growth.values[0]/solution_original)
+            df_sensitivity.loc[model_name] = newRow
+            df_sensitivity = df_sensitivity.astype(float).round(6)
+    return df_pFBA, df_FVA, df_sensitivity
+
 ############################# main ###########################################
 def main() -> None:
     """
@@ -221,26 +308,30 @@
     Returns:
         None
     """
-    if not os.path.exists('flux_sampling'):
-        os.makedirs('flux_sampling')
+    if not os.path.exists('flux_simulation/'):
+        os.makedirs('flux_simulation/')
 
     num_processors = cpu_count()
 
     global ARGS
     ARGS = process_args(sys.argv)
 
-    ARGS.output_folder = 'flux_sampling/'
+    ARGS.output_folder = 'flux_simulation/'
     
-    utils.logWarning(
-        ARGS.output_type,
-        ARGS.out_log)
     
-    models_input = ARGS.input.split(",")
-    models_name = ARGS.name.split(",")
+    model_type :utils.Model = ARGS.model_selector
+    if model_type is utils.Model.Custom:
+        model = model_type.getCOBRAmodel(customPath = utils.FilePath.fromStrPath(ARGS.model), customExtension = utils.FilePath.fromStrPath(ARGS.model_name).ext)
+    else:
+        model = model_type.getCOBRAmodel(toolDir=ARGS.tool_dir)
+    
+    ARGS.bounds = ARGS.input.split(",")
+    ARGS.bounds_name = ARGS.names.split(",")
     ARGS.output_types = ARGS.output_type.split(",")
+    ARGS.output_type_analysis = ARGS.output_type_analysis.split(",")
 
- 
-    results = Parallel(n_jobs=num_processors)(delayed(model_sampler)(model_input, model_name) for model_input, model_name in zip(models_input, models_name))
+
+    results = Parallel(n_jobs=num_processors)(delayed(model_sampler)(model, bounds_path, cell_name) for bounds_path, cell_name in zip(ARGS.bounds, ARGS.bounds_name))
 
     all_mean = pd.concat([result[0] for result in results], ignore_index=False)
     all_median = pd.concat([result[1] for result in results], ignore_index=False)
@@ -260,6 +351,23 @@
         all_quantiles = all_quantiles.fillna(0.0)
         all_quantiles = all_quantiles.sort_index()
         write_to_file(all_quantiles, "quantiles", True)
+
+    index_result = 3
+    if("pFBA" in ARGS.output_type_analysis):
+        all_pFBA = pd.concat([result[index_result] for result in results], ignore_index=False)
+        all_pFBA = all_pFBA.sort_index()
+        write_to_file(all_pFBA, "pFBA", True)
+        index_result+=1
+    if("FVA" in ARGS.output_type_analysis):
+        all_FVA= pd.concat([result[index_result] for result in results], ignore_index=False)
+        all_FVA = all_FVA.sort_index()
+        write_to_file(all_FVA, "FVA", True)
+        index_result+=1
+    if("sensitivity" in ARGS.output_type_analysis):
+        all_sensitivity = pd.concat([result[index_result] for result in results], ignore_index=False)
+        all_sensitivity = all_sensitivity.sort_index()
+        write_to_file(all_sensitivity, "sensitivity", True)
+
     pass
         
 ##############################################################################