annotate COBRAxy/ras_to_bounds_beta.py @ 407:6619f237aebe draft

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author francesco_lapi
date Mon, 08 Sep 2025 16:52:46 +0000
parents 187cee1a00e2
children f413b78d61bf
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1 import argparse
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2 import utils.general_utils as utils
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3 from typing import Optional, Dict, Set, List, Tuple
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4 import os
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5 import numpy as np
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6 import pandas as pd
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7 import cobra
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8 from cobra import Model, Reaction, Metabolite
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9 import re
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10 import sys
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11 import csv
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12 from joblib import Parallel, delayed, cpu_count
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13
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14 # , medium
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15
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16 ################################# process args ###############################
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17 def process_args(args :List[str] = None) -> argparse.Namespace:
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18 """
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19 Processes command-line arguments.
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20
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21 Args:
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22 args (list): List of command-line arguments.
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23
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24 Returns:
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25 Namespace: An object containing parsed arguments.
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26 """
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27 parser = argparse.ArgumentParser(usage = '%(prog)s [options]',
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28 description = 'process some value\'s')
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29
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30
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31 parser.add_argument("-mo", "--model_upload", type = str,
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32 help = "path to input file with custom rules, if provided")
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33
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34 parser.add_argument("-meo", "--medium", type = str,
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35 help = "path to input file with custom medium, if provided")
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36
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37 parser.add_argument('-ol', '--out_log',
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38 help = "Output log")
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39
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40 parser.add_argument('-td', '--tool_dir',
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41 type = str,
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42 required = True,
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43 help = 'your tool directory')
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44
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45 parser.add_argument('-ir', '--input_ras',
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46 type=str,
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47 required = False,
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48 help = 'input ras')
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49
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50 parser.add_argument('-rn', '--name',
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51 type=str,
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52 help = 'ras class names')
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53
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54 parser.add_argument('-rs', '--ras_selector',
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55 required = True,
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56 type=utils.Bool("using_RAS"),
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57 help = 'ras selector')
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58
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59 parser.add_argument('-cc', '--cell_class',
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60 type = str,
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61 help = 'output of cell class')
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62 parser.add_argument(
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63 '-idop', '--output_path',
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64 type = str,
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65 default='ras_to_bounds/',
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66 help = 'output path for maps')
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67
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68
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69 ARGS = parser.parse_args(args)
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70 return ARGS
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71
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72 ########################### warning ###########################################
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73 def warning(s :str) -> None:
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74 """
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75 Log a warning message to an output log file and print it to the console.
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76
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77 Args:
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78 s (str): The warning message to be logged and printed.
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79
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80 Returns:
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81 None
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82 """
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83 with open(ARGS.out_log, 'a') as log:
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84 log.write(s + "\n\n")
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85 print(s)
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86
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87 ############################ dataset input ####################################
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88 def read_dataset(data :str, name :str) -> pd.DataFrame:
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89 """
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90 Read a dataset from a CSV file and return it as a pandas DataFrame.
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91
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92 Args:
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93 data (str): Path to the CSV file containing the dataset.
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94 name (str): Name of the dataset, used in error messages.
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95
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96 Returns:
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97 pandas.DataFrame: DataFrame containing the dataset.
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98
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99 Raises:
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100 pd.errors.EmptyDataError: If the CSV file is empty.
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101 sys.exit: If the CSV file has the wrong format, the execution is aborted.
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102 """
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103 try:
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104 dataset = pd.read_csv(data, sep = '\t', header = 0, engine='python')
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105 except pd.errors.EmptyDataError:
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106 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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107 if len(dataset.columns) < 2:
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108 sys.exit('Execution aborted: wrong format of ' + name + '\n')
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109 return dataset
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110
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111
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112 def apply_ras_bounds(bounds, ras_row):
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113 """
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114 Adjust the bounds of reactions in the model based on RAS values.
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115
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116 Args:
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117 bounds (pd.DataFrame): Model bounds.
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118 ras_row (pd.Series): A row from a RAS DataFrame containing scaling factors for reaction bounds.
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119 Returns:
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120 new_bounds (pd.DataFrame): integrated bounds.
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121 """
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122 new_bounds = bounds.copy()
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123 for reaction in ras_row.index:
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124 scaling_factor = ras_row[reaction]
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125 if not np.isnan(scaling_factor):
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126 lower_bound=bounds.loc[reaction, "lower_bound"]
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127 upper_bound=bounds.loc[reaction, "upper_bound"]
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128 valMax=float((upper_bound)*scaling_factor)
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129 valMin=float((lower_bound)*scaling_factor)
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130 if upper_bound!=0 and lower_bound==0:
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131 new_bounds.loc[reaction, "upper_bound"] = valMax
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132 if upper_bound==0 and lower_bound!=0:
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133 new_bounds.loc[reaction, "lower_bound"] = valMin
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134 if upper_bound!=0 and lower_bound!=0:
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135 new_bounds.loc[reaction, "lower_bound"] = valMin
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136 new_bounds.loc[reaction, "upper_bound"] = valMax
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137 return new_bounds
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138
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139 def process_ras_cell(cellName, ras_row, model, rxns_ids, output_folder):
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140 """
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141 Process a single RAS cell, apply bounds, and save the bounds to a CSV file.
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142
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143 Args:
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144 cellName (str): The name of the RAS cell (used for naming the output file).
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145 ras_row (pd.Series): A row from a RAS DataFrame containing scaling factors for reaction bounds.
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146 model (cobra.Model): The metabolic model to be modified.
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147 rxns_ids (list of str): List of reaction IDs to which the scaling factors will be applied.
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148 output_folder (str): Folder path where the output CSV file will be saved.
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149
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150 Returns:
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151 None
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152 """
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153 bounds = pd.DataFrame([(rxn.lower_bound, rxn.upper_bound) for rxn in model.reactions], index=rxns_ids, columns=["lower_bound", "upper_bound"])
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154 new_bounds = apply_ras_bounds(bounds, ras_row)
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155 new_bounds.to_csv(output_folder + cellName + ".csv", sep='\t', index=True)
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156 pass
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157
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158 def generate_bounds(model: cobra.Model, ras=None, output_folder='output/') -> pd.DataFrame:
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159 """
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160 Generate reaction bounds for a metabolic model based on medium conditions and optional RAS adjustments.
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161
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162 Args:
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163 model (cobra.Model): The metabolic model for which bounds will be generated.
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164 medium (dict): A dictionary where keys are reaction IDs and values are the medium conditions.
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165 ras (pd.DataFrame, optional): RAS pandas dataframe. Defaults to None.
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166 output_folder (str, optional): Folder path where output CSV files will be saved. Defaults to 'output/'.
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167
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168 Returns:
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169 pd.DataFrame: DataFrame containing the bounds of reactions in the model.
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170 """
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171 rxns_ids = [rxn.id for rxn in model.reactions]
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172
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173 # Perform Flux Variability Analysis (FVA) on this medium
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174 df_FVA = cobra.flux_analysis.flux_variability_analysis(model, fraction_of_optimum=0, processes=1).round(8)
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175
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176 # Set FVA bounds
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177 for reaction in rxns_ids:
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178 model.reactions.get_by_id(reaction).lower_bound = float(df_FVA.loc[reaction, "minimum"])
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179 model.reactions.get_by_id(reaction).upper_bound = float(df_FVA.loc[reaction, "maximum"])
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180
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181 if ras is not None:
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182 Parallel(n_jobs=cpu_count())(delayed(process_ras_cell)(cellName, ras_row, model, rxns_ids, output_folder) for cellName, ras_row in ras.iterrows())
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183 else:
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184 bounds = pd.DataFrame([(rxn.lower_bound, rxn.upper_bound) for rxn in model.reactions], index=rxns_ids, columns=["lower_bound", "upper_bound"])
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185 newBounds = apply_ras_bounds(bounds, pd.Series([1]*len(rxns_ids), index=rxns_ids))
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186 newBounds.to_csv(output_folder + "bounds.csv", sep='\t', index=True)
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187 pass
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188
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189 # TODO: VALUTARE QUALI DI QUESTE FUNZIONI METTERE IN UTILS.PY
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190 def build_cobra_model_from_csv(csv_path: str, model_id: str = "ENGRO2_custom") -> cobra.Model:
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191 """
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192 Costruisce un modello COBRApy a partire da un file CSV con i dati delle reazioni.
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193
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194 Args:
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195 csv_path: Path al file CSV (separato da tab)
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196 model_id: ID del modello da creare
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197
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198 Returns:
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199 cobra.Model: Il modello COBRApy costruito
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200 """
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201
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202 # Leggi i dati dal CSV
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203 df = pd.read_csv(csv_path, sep='\t')
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204
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205 # Crea il modello vuoto
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206 model = Model(model_id)
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207
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208 # Dict per tenere traccia di metaboliti e compartimenti
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209 metabolites_dict = {}
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210 compartments_dict = {}
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211
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212 print(f"Costruendo modello da {len(df)} reazioni...")
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213
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214 # Prima passata: estrai metaboliti e compartimenti dalle formule delle reazioni
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215 for idx, row in df.iterrows():
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216 reaction_formula = str(row['Reaction']).strip()
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217 if not reaction_formula or reaction_formula == 'nan':
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218 continue
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219
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220 # Estrai metaboliti dalla formula della reazione
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221 metabolites = extract_metabolites_from_reaction(reaction_formula)
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222
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223 for met_id in metabolites:
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224 compartment = extract_compartment_from_metabolite(met_id)
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225
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226 # Aggiungi compartimento se non esiste
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227 if compartment not in compartments_dict:
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228 compartments_dict[compartment] = compartment
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229
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230 # Aggiungi metabolita se non esiste
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231 if met_id not in metabolites_dict:
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232 metabolites_dict[met_id] = Metabolite(
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233 id=met_id,
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234 compartment=compartment,
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235 name=met_id.replace(f"_{compartment}", "").replace("__", "_")
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236 )
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237
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238 # Aggiungi compartimenti al modello
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239 model.compartments = compartments_dict
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240
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241 # Aggiungi metaboliti al modello
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242 model.add_metabolites(list(metabolites_dict.values()))
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243
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244 print(f"Aggiunti {len(metabolites_dict)} metaboliti e {len(compartments_dict)} compartimenti")
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245
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246 # Seconda passata: aggiungi le reazioni
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247 reactions_added = 0
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248 reactions_skipped = 0
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249
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250 for idx, row in df.iterrows():
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251 try:
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252 reaction_id = str(row['ReactionID']).strip()
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253 if reaction_id == 'EX_thbpt_e':
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254 print('qui')
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255 print(reaction_id)
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256 print(str(row['Reaction']).strip())
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257 print('qui')
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258 reaction_formula = str(row['Reaction']).strip()
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259
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260 # Salta reazioni senza formula
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261 if not reaction_formula or reaction_formula == 'nan':
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262 reactions_skipped += 1
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263 continue
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264
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265 # Crea la reazione
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266 reaction = Reaction(reaction_id)
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267 reaction.name = reaction_id
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268
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269 # Imposta bounds
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270 reaction.lower_bound = float(row['lower_bound']) if pd.notna(row['lower_bound']) else -1000.0
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271 reaction.upper_bound = float(row['upper_bound']) if pd.notna(row['upper_bound']) else 1000.0
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272
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273 # Aggiungi gene rule se presente
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274 if pd.notna(row['Rule']) and str(row['Rule']).strip():
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275 reaction.gene_reaction_rule = str(row['Rule']).strip()
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276
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277 # Parse della formula della reazione
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278 try:
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279 parse_reaction_formula(reaction, reaction_formula, metabolites_dict)
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280 except Exception as e:
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281 print(f"Errore nel parsing della reazione {reaction_id}: {e}")
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282 reactions_skipped += 1
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283 continue
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284
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285 # Aggiungi la reazione al modello
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286 model.add_reactions([reaction])
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287 reactions_added += 1
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288
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289 except Exception as e:
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290 print(f"Errore nell'aggiungere la reazione {reaction_id}: {e}")
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291 reactions_skipped += 1
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292 continue
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293
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294 print(f"Aggiunte {reactions_added} reazioni, saltate {reactions_skipped} reazioni")
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295
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296 # Imposta l'obiettivo di biomassa
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297 set_biomass_objective(model)
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298
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299 # Imposta il medium
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300 set_medium_from_data(model, df)
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301
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302 print(f"Modello completato: {len(model.reactions)} reazioni, {len(model.metabolites)} metaboliti")
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303
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304 return model
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305
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306
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307 # Estrae tutti gli ID metaboliti nella formula (gestisce prefissi numerici + underscore)
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308 def extract_metabolites_from_reaction(reaction_formula: str) -> Set[str]:
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309 """
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310 Estrae gli ID dei metaboliti da una formula di reazione.
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311 Pattern robusto: cattura token che terminano con _<compartimento> (es. _c, _m, _e)
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312 e permette che comincino con cifre o underscore.
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313 """
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314 metabolites = set()
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315 # coefficiente opzionale seguito da un token che termina con _<letters>
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316 pattern = r'(?:\d+(?:\.\d+)?\s+)?([A-Za-z0-9_]+_[a-z]+)'
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317 matches = re.findall(pattern, reaction_formula)
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318 metabolites.update(matches)
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319 return metabolites
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320
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321
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322 def extract_compartment_from_metabolite(metabolite_id: str) -> str:
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323 """
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324 Estrae il compartimento dall'ID del metabolita.
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325 """
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326 # Il compartimento è solitamente l'ultima lettera dopo l'underscore
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327 if '_' in metabolite_id:
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328 return metabolite_id.split('_')[-1]
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329 return 'c' # default cytoplasm
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330
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331
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332 def parse_reaction_formula(reaction: Reaction, formula: str, metabolites_dict: Dict[str, Metabolite]):
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333 """
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334 Parsa una formula di reazione e imposta i metaboliti con i loro coefficienti.
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335 """
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336
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337 if reaction.id == 'EX_thbpt_e':
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338 print(reaction.id)
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339 print(formula)
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340 # Dividi in parte sinistra e destra
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341 if '<=>' in formula:
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342 left, right = formula.split('<=>')
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343 reversible = True
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344 elif '<--' in formula:
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345 left, right = formula.split('<--')
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346 reversible = False
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347 left, right = left, right
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348 elif '-->' in formula:
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349 left, right = formula.split('-->')
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350 reversible = False
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351 elif '<-' in formula:
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352 left, right = formula.split('<-')
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353 reversible = False
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354 left, right = left, right
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355 else:
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356 raise ValueError(f"Formato reazione non riconosciuto: {formula}")
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357
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358 # Parse dei metaboliti e coefficienti
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359 reactants = parse_metabolites_side(left.strip())
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360 products = parse_metabolites_side(right.strip())
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361
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362 # Aggiungi metaboliti alla reazione
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363 metabolites_to_add = {}
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364
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365 # Reagenti (coefficienti negativi)
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366 for met_id, coeff in reactants.items():
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367 if met_id in metabolites_dict:
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368 metabolites_to_add[metabolites_dict[met_id]] = -coeff
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369
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370 # Prodotti (coefficienti positivi)
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371 for met_id, coeff in products.items():
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372 if met_id in metabolites_dict:
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373 metabolites_to_add[metabolites_dict[met_id]] = coeff
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374
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375 reaction.add_metabolites(metabolites_to_add)
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376
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377
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378 def parse_metabolites_side(side_str: str) -> Dict[str, float]:
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379 """
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380 Parsa un lato della reazione per estrarre metaboliti e coefficienti.
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381 """
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382 metabolites = {}
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383 if not side_str or side_str.strip() == '':
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384 return metabolites
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385
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386 terms = side_str.split('+')
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387 for term in terms:
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388 term = term.strip()
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389 if not term:
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390 continue
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391
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392 # pattern allineato: coefficiente opzionale + id che termina con _<compartimento>
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393 match = re.match(r'(?:(\d+\.?\d*)\s+)?([A-Za-z0-9_]+_[a-z]+)', term)
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394 if match:
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395 coeff_str, met_id = match.groups()
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396 coeff = float(coeff_str) if coeff_str else 1.0
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397 metabolites[met_id] = coeff
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398
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399 return metabolites
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400
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401
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402
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403 def set_biomass_objective(model: Model):
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404 """
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405 Imposta la reazione di biomassa come obiettivo.
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406 """
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407 biomass_reactions = [r for r in model.reactions if 'biomass' in r.id.lower()]
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408
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409 if biomass_reactions:
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410 model.objective = biomass_reactions[0].id
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411 print(f"Obiettivo impostato su: {biomass_reactions[0].id}")
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412 else:
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413 print("Nessuna reazione di biomassa trovata")
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414
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415
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416 def set_medium_from_data(model: Model, df: pd.DataFrame):
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417 """
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418 Imposta il medium basato sulla colonna InMedium.
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419 """
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420 medium_reactions = df[df['InMedium'] == True]['ReactionID'].tolist()
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421
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422 medium_dict = {}
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423 for rxn_id in medium_reactions:
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424 if rxn_id in [r.id for r in model.reactions]:
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425 reaction = model.reactions.get_by_id(rxn_id)
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426 if reaction.lower_bound < 0: # Solo reazioni di uptake
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427 medium_dict[rxn_id] = abs(reaction.lower_bound)
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428
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429 if medium_dict:
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430 model.medium = medium_dict
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431 print(f"Medium impostato con {len(medium_dict)} componenti")
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432
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433
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434 def validate_model(model: Model) -> Dict[str, any]:
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435 """
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436 Valida il modello e fornisce statistiche di base.
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437 """
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438 validation = {
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439 'num_reactions': len(model.reactions),
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440 'num_metabolites': len(model.metabolites),
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441 'num_genes': len(model.genes),
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442 'num_compartments': len(model.compartments),
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443 'objective': str(model.objective),
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444 'medium_size': len(model.medium),
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445 'reversible_reactions': len([r for r in model.reactions if r.reversibility]),
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446 'exchange_reactions': len([r for r in model.reactions if r.id.startswith('EX_')]),
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447 }
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448
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449 try:
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450 # Test di crescita
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451 solution = model.optimize()
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452 validation['growth_rate'] = solution.objective_value
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453 validation['status'] = solution.status
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454 except Exception as e:
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455 validation['growth_rate'] = None
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456 validation['status'] = f"Error: {e}"
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457
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458 return validation
406
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459
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460
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461 ############################# main ###########################################
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462 def main(args:List[str] = None) -> None:
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463 """
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464 Initializes everything and sets the program in motion based on the fronted input arguments.
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465
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466 Returns:
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467 None
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468 """
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469 if not os.path.exists('ras_to_bounds'):
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470 os.makedirs('ras_to_bounds')
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471
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472
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473 global ARGS
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474 ARGS = process_args(args)
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475
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476 if(ARGS.ras_selector == True):
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477 ras_file_list = ARGS.input_ras.split(",")
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478 ras_file_names = ARGS.name.split(",")
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479 if len(ras_file_names) != len(set(ras_file_names)):
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480 error_message = "Duplicated file names in the uploaded RAS matrices."
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481 warning(error_message)
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482 raise ValueError(error_message)
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483 pass
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484 ras_class_names = []
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485 for file in ras_file_names:
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486 ras_class_names.append(file.rsplit(".", 1)[0])
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487 ras_list = []
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488 class_assignments = pd.DataFrame(columns=["Patient_ID", "Class"])
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489 for ras_matrix, ras_class_name in zip(ras_file_list, ras_class_names):
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490 ras = read_dataset(ras_matrix, "ras dataset")
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491 ras.replace("None", None, inplace=True)
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492 ras.set_index("Reactions", drop=True, inplace=True)
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493 ras = ras.T
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494 ras = ras.astype(float)
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495 if(len(ras_file_list)>1):
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496 #append class name to patient id (dataframe index)
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497 ras.index = [f"{idx}_{ras_class_name}" for idx in ras.index]
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498 else:
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499 ras.index = [f"{idx}" for idx in ras.index]
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500 ras_list.append(ras)
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501 for patient_id in ras.index:
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502 class_assignments.loc[class_assignments.shape[0]] = [patient_id, ras_class_name]
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503
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504
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505 # Concatenate all ras DataFrames into a single DataFrame
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506 ras_combined = pd.concat(ras_list, axis=0)
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507 # Normalize the RAS values by max RAS
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508 ras_combined = ras_combined.div(ras_combined.max(axis=0))
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509 ras_combined.dropna(axis=1, how='all', inplace=True)
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510
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511
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512
407
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513 #model_type :utils.Model = ARGS.model_selector
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514 #if model_type is utils.Model.Custom:
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515 # model = model_type.getCOBRAmodel(customPath = utils.FilePath.fromStrPath(ARGS.model), customExtension = utils.FilePath.fromStrPath(ARGS.model_name).ext)
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516 #else:
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517 # model = model_type.getCOBRAmodel(toolDir=ARGS.tool_dir)
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518
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diff changeset
519 # TODO LOAD MODEL FROM UPLOAD
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520
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521 model = build_cobra_model_from_csv(ARGS.model_upload)
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522
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523 validation = validate_model(model)
406
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524
407
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525 print("\n=== VALIDAZIONE MODELLO ===")
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526 for key, value in validation.items():
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527 print(f"{key}: {value}")
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528
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diff changeset
529 #if(ARGS.medium_selector == "Custom"):
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530 # medium = read_dataset(ARGS.medium, "medium dataset")
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diff changeset
531 # medium.set_index(medium.columns[0], inplace=True)
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532 # medium = medium.astype(float)
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533 # medium = medium[medium.columns[0]].to_dict()
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534 #else:
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diff changeset
535 # df_mediums = pd.read_csv(ARGS.tool_dir + "/local/medium/medium.csv", index_col = 0)
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diff changeset
536 # ARGS.medium_selector = ARGS.medium_selector.replace("_", " ")
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diff changeset
537 # medium = df_mediums[[ARGS.medium_selector]]
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diff changeset
538 # medium = medium[ARGS.medium_selector].to_dict()
406
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539
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540 if(ARGS.ras_selector == True):
407
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diff changeset
541 generate_bounds(model, ras = ras_combined, output_folder=ARGS.output_path)
406
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542 class_assignments.to_csv(ARGS.cell_class, sep = '\t', index = False)
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diff changeset
543 else:
407
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diff changeset
544 generate_bounds(model, output_folder=ARGS.output_path)
406
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545
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diff changeset
546 pass
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547
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548 ##############################################################################
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549 if __name__ == "__main__":
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550 main()