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comparison COBRAxy/metabolic_model_setting.py @ 457:5b625d91bc7f draft

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author francesco_lapi
date Wed, 17 Sep 2025 14:26:58 +0000
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456:a6e45049c1b9 457:5b625d91bc7f
1 """
2 Scripts to generate a tabular file of a metabolic model (built-in or custom).
3
4 This script loads a COBRA model (built-in or custom), optionally applies
5 medium and gene nomenclature settings, derives reaction-related metadata
6 (GPR rules, formulas, bounds, objective coefficients, medium membership,
7 and compartments for ENGRO2), and writes a tabular summary.
8 """
9
10 import os
11 import csv
12 import cobra
13 import argparse
14 import pandas as pd
15 import utils.general_utils as utils
16 from typing import Optional, Tuple, List
17 import utils.model_utils as modelUtils
18 import logging
19
20 ARGS : argparse.Namespace
21 def process_args(args: List[str] = None) -> argparse.Namespace:
22 """
23 Parse command-line arguments for metabolic_model_setting.
24 """
25
26 parser = argparse.ArgumentParser(
27 usage="%(prog)s [options]",
28 description="Generate custom data from a given model"
29 )
30
31 parser.add_argument("--out_log", type=str, required=True,
32 help="Output log file")
33
34 parser.add_argument("--model", type=str,
35 help="Built-in model identifier (e.g., ENGRO2, Recon, HMRcore)")
36 parser.add_argument("--input", type=str,
37 help="Custom model file (JSON or XML)")
38 parser.add_argument("--name", type=str, required=True,
39 help="Model name (default or custom)")
40
41 parser.add_argument("--medium_selector", type=str, required=True,
42 help="Medium selection option")
43
44 parser.add_argument("--gene_format", type=str, default="Default",
45 help="Gene nomenclature format: Default (original), ENSNG, HGNC_SYMBOL, HGNC_ID, ENTREZ")
46
47 parser.add_argument("--out_tabular", type=str,
48 help="Output file for the merged dataset (CSV or XLSX)")
49
50 parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
51 help="Tool directory (passed from Galaxy as $__tool_directory__)")
52
53
54 return parser.parse_args(args)
55
56 ################################- INPUT DATA LOADING -################################
57 def load_custom_model(file_path :utils.FilePath, ext :Optional[utils.FileFormat] = None) -> cobra.Model:
58 """
59 Loads a custom model from a file, either in JSON, XML, MAT, or YML format.
60
61 Args:
62 file_path : The path to the file containing the custom model.
63 ext : explicit file extension. Necessary for standard use in galaxy because of its weird behaviour.
64
65 Raises:
66 DataErr : if the file is in an invalid format or cannot be opened for whatever reason.
67
68 Returns:
69 cobra.Model : the model, if successfully opened.
70 """
71 ext = ext if ext else file_path.ext
72 try:
73 if ext is utils.FileFormat.XML:
74 return cobra.io.read_sbml_model(file_path.show())
75
76 if ext is utils.FileFormat.JSON:
77 return cobra.io.load_json_model(file_path.show())
78
79 if ext is utils.FileFormat.MAT:
80 return cobra.io.load_matlab_model(file_path.show())
81
82 if ext is utils.FileFormat.YML:
83 return cobra.io.load_yaml_model(file_path.show())
84
85 except Exception as e: raise utils.DataErr(file_path, e.__str__())
86 raise utils.DataErr(
87 file_path,
88 f"Unrecognized format '{file_path.ext}'. Only JSON, XML, MAT, YML are supported."
89 )
90
91
92 ###############################- FILE SAVING -################################
93 def save_as_csv_filePath(data :dict, file_path :utils.FilePath, fieldNames :Tuple[str, str]) -> None:
94 """
95 Saves any dictionary-shaped data in a .csv file created at the given file_path as FilePath.
96
97 Args:
98 data : the data to be written to the file.
99 file_path : the path to the .csv file.
100 fieldNames : the names of the fields (columns) in the .csv file.
101
102 Returns:
103 None
104 """
105 with open(file_path.show(), 'w', newline='') as csvfile:
106 writer = csv.DictWriter(csvfile, fieldnames = fieldNames, dialect="excel-tab")
107 writer.writeheader()
108
109 for key, value in data.items():
110 writer.writerow({ fieldNames[0] : key, fieldNames[1] : value })
111
112 def save_as_csv(data :dict, file_path :str, fieldNames :Tuple[str, str]) -> None:
113 """
114 Saves any dictionary-shaped data in a .csv file created at the given file_path as string.
115
116 Args:
117 data : the data to be written to the file.
118 file_path : the path to the .csv file.
119 fieldNames : the names of the fields (columns) in the .csv file.
120
121 Returns:
122 None
123 """
124 with open(file_path, 'w', newline='') as csvfile:
125 writer = csv.DictWriter(csvfile, fieldnames = fieldNames, dialect="excel-tab")
126 writer.writeheader()
127
128 for key, value in data.items():
129 writer.writerow({ fieldNames[0] : key, fieldNames[1] : value })
130
131 def save_as_tabular_df(df: pd.DataFrame, path: str) -> None:
132 """
133 Save a pandas DataFrame as a tab-separated file, creating directories as needed.
134
135 Args:
136 df: The DataFrame to write.
137 path: Destination file path (will be written as TSV).
138
139 Raises:
140 DataErr: If writing the output fails for any reason.
141
142 Returns:
143 None
144 """
145 try:
146 os.makedirs(os.path.dirname(path) or ".", exist_ok=True)
147 df.to_csv(path, sep="\t", index=False)
148 except Exception as e:
149 raise utils.DataErr(path, f"failed writing tabular output: {e}")
150
151
152 ###############################- ENTRY POINT -################################
153 def main(args:List[str] = None) -> None:
154 """
155 Initialize and generate custom data based on the frontend input arguments.
156
157 Returns:
158 None
159 """
160 # Parse args from frontend (Galaxy XML)
161 global ARGS
162 ARGS = process_args(args)
163
164
165 if ARGS.input:
166 # Load a custom model from file
167 model = load_custom_model(
168 utils.FilePath.fromStrPath(ARGS.input), utils.FilePath.fromStrPath(ARGS.name).ext)
169 else:
170 # Load a built-in model
171
172 try:
173 model_enum = utils.Model[ARGS.model] # e.g., Model['ENGRO2']
174 except KeyError:
175 raise utils.ArgsErr("model", "one of Recon/ENGRO2/HMRcore/Custom_model", ARGS.model)
176
177 # Load built-in model (Model.getCOBRAmodel uses tool_dir to locate local models)
178 try:
179 model = model_enum.getCOBRAmodel(toolDir=ARGS.tool_dir)
180 except Exception as e:
181 # Wrap/normalize load errors as DataErr for consistency
182 raise utils.DataErr(ARGS.model, f"failed loading built-in model: {e}")
183
184 # Determine final model name: explicit --name overrides, otherwise use the model id
185
186 model_name = ARGS.name if ARGS.name else ARGS.model
187
188 if ARGS.name == "ENGRO2" and ARGS.medium_selector != "Default":
189 df_mediums = pd.read_csv(ARGS.tool_dir + "/local/medium/medium.csv", index_col = 0)
190 ARGS.medium_selector = ARGS.medium_selector.replace("_", " ")
191 medium = df_mediums[[ARGS.medium_selector]]
192 medium = medium[ARGS.medium_selector].to_dict()
193
194 # Reset all medium reactions lower bound to zero
195 for rxn_id, _ in model.medium.items():
196 model.reactions.get_by_id(rxn_id).lower_bound = float(0.0)
197
198 # Apply selected medium uptake bounds (negative for uptake)
199 for reaction, value in medium.items():
200 if value is not None:
201 model.reactions.get_by_id(reaction).lower_bound = -float(value)
202
203 if (ARGS.name == "Recon" or ARGS.name == "ENGRO2") and ARGS.gene_format != "Default":
204 logging.basicConfig(level=logging.INFO)
205 logger = logging.getLogger(__name__)
206
207 model = modelUtils.translate_model_genes(
208 model=model,
209 mapping_df= pd.read_csv(ARGS.tool_dir + "/local/mappings/genes_human.csv", dtype={'entrez_id': str}),
210 target_nomenclature=ARGS.gene_format,
211 source_nomenclature='HGNC_symbol',
212 logger=logger
213 )
214
215 # generate data
216 rules = modelUtils.generate_rules(model, asParsed = False)
217 reactions = modelUtils.generate_reactions(model, asParsed = False)
218 bounds = modelUtils.generate_bounds(model)
219 medium = modelUtils.get_medium(model)
220 objective_function = modelUtils.extract_objective_coefficients(model)
221
222 if ARGS.name == "ENGRO2":
223 compartments = modelUtils.generate_compartments(model)
224
225 df_rules = pd.DataFrame(list(rules.items()), columns = ["ReactionID", "GPR"])
226 df_reactions = pd.DataFrame(list(reactions.items()), columns = ["ReactionID", "Formula"])
227
228 df_bounds = bounds.reset_index().rename(columns = {"index": "ReactionID"})
229 df_medium = medium.rename(columns = {"reaction": "ReactionID"})
230 df_medium["InMedium"] = True
231
232 merged = df_reactions.merge(df_rules, on = "ReactionID", how = "outer")
233 merged = merged.merge(df_bounds, on = "ReactionID", how = "outer")
234 merged = merged.merge(objective_function, on = "ReactionID", how = "outer")
235 if ARGS.name == "ENGRO2":
236 merged = merged.merge(compartments, on = "ReactionID", how = "outer")
237 merged = merged.merge(df_medium, on = "ReactionID", how = "left")
238
239 merged["InMedium"] = merged["InMedium"].fillna(False)
240
241 merged = merged.sort_values(by = "InMedium", ascending = False)
242
243 if not ARGS.out_tabular:
244 raise utils.ArgsErr("out_tabular", "output path (--out_tabular) is required when output_format == tabular", ARGS.out_tabular)
245 save_as_tabular_df(merged, ARGS.out_tabular)
246 expected = ARGS.out_tabular
247
248 # verify output exists and non-empty
249 if not expected or not os.path.exists(expected) or os.path.getsize(expected) == 0:
250 raise utils.DataErr(expected, "Output not created or empty")
251
252 print("Metabolic_model_setting: completed successfully")
253
254 if __name__ == '__main__':
255
256 main()