diff gem_flux_variability_analysis.py @ 0:dfeabe31d865 draft default tip

planemo upload for repository https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology commit 3f7bec1264a86e1488ee1315dbac0f44675f5171

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gem_flux_variability_analysis.py	Fri Dec 13 21:34:04 2024 +0000
@@ -0,0 +1,121 @@
+import argparse
+
+import cobra
+import pandas as pd
+
+
+def __main__():
+    parser = argparse.ArgumentParser(
+        prog="FluxVariabilityAnalysis",
+        description="This program performs flux variability "
+        "analysis on a GEM",
+        epilog="Adding an epilog, but doubt it's needed.",
+    )
+    parser.add_argument(
+        "-m", "--cb_model_location",
+        dest="cb_model_location",
+        action="store",
+        type=str,
+        default=None,
+        required=True,
+        help="The model to use."
+    )
+    parser.add_argument(
+        "-output",
+        "--output",
+        dest="out_file",
+        action="store",
+        type=str,
+        default=None,
+        required=True,
+        help="The output file."
+    )
+    parser.add_argument(
+        "-f",
+        "--fraction",
+        dest="fraction_of_optimum",
+        action="store",
+        type=float,
+        default=None,
+        required=True,
+        help="The fraction of optimum the FVA solutions should come within."
+    )
+    parser.add_argument(
+        "-u",
+        "--uptake_constraints_file",
+        dest="uptake_constraints_file",
+        action="store",
+        type=str,
+        default=None,
+        required=False,
+        help="File containing new uptake constraits."
+    )
+
+    args = parser.parse_args()
+
+    # Validate constraints file first if provided
+    constraints_df = None
+    if args.uptake_constraints_file is not None\
+            and args.uptake_constraints_file != "None":
+        try:
+            constraints_df = pd.read_csv(
+                args.uptake_constraints_file,
+                sep=";",
+                header=0,
+                index_col=False
+            )
+
+            required_columns = ['reaction_id', 'lower_bound', 'upper_bound']
+            missing_columns = [col for col in required_columns if
+                               col not in constraints_df.columns]
+
+            if missing_columns:
+                raise ValueError(
+                    f"Constraints file is missing required columns: "
+                    f"{', '.join(missing_columns)}. "
+                    f"Required columns are: {', '.join(required_columns)}"
+                )
+        except FileNotFoundError:
+            raise FileNotFoundError(
+                f"Constraints file not found: {args.uptake_constraints_file}"
+            )
+        except pd.errors.EmptyDataError:
+            raise ValueError("Constraints file is empty")
+        except Exception as e:
+            raise ValueError(f"Error processing constraints file: {str(e)}")
+
+    # Load model
+    cb_model = cobra.io.read_sbml_model(args.cb_model_location)
+
+    # Apply constraints if they were loaded successfully
+    if constraints_df is not None:
+        for index, row in constraints_df.iterrows():
+            cb_model.reactions.get_by_id(
+                row["reaction_id"]).lower_bound = float(row["lower_bound"])
+            cb_model.reactions.get_by_id(
+                row["reaction_id"]).upper_bound = float(row["upper_bound"])
+
+    fraction_of_optimum = args.fraction_of_optimum
+
+    # perform fva
+    fva_result = cobra.flux_analysis.flux_variability_analysis(
+        cb_model,
+        fraction_of_optimum=fraction_of_optimum
+    )
+
+    # add reaction names and ids to the dataframe
+    fva_result["reaction_id"] = fva_result.index
+    fva_result["reaction_name"] = fva_result["reaction_id"].apply(
+        lambda x: cb_model.reactions.get_by_id(x).name
+    )
+
+    # reorder the columns
+    fva_result = fva_result[[
+        "reaction_id", "reaction_name", "minimum", "maximum"
+    ]]
+
+    fva_result.to_csv(args.out_file, sep=";", index=False, header=True)
+
+
+if __name__ == "__main__":
+    __main__()