diff gem_extract_exchange.py @ 0:d9893d41dd6a 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_extract_exchange.py	Fri Dec 13 21:33:34 2024 +0000
@@ -0,0 +1,80 @@
+import argparse
+
+import cobra
+
+
+def read_model(model_location):
+    model = cobra.io.read_sbml_model(model_location)
+    return model
+
+
+def get_exchange_reactions_info(model):
+    exchange_reactions = model.exchanges
+    exchange_reactions_info = []
+    for reaction in exchange_reactions:
+        exchange_reactions_info.append(
+            [
+                reaction.id,
+                reaction.name,
+                reaction.reaction,
+                reaction.lower_bound,
+                reaction.upper_bound
+            ])
+    txt_object = (
+        "reaction_id;reaction_name;reaction_stoichiometry;"
+        "lower_bound;upper_bound\n"
+    )
+    for reaction in exchange_reactions_info:
+        txt_object += ";".join([str(x) for x in reaction]) + "\n"
+    return txt_object
+
+
+def __main__():
+
+    # Parsing arguments
+    parser = argparse.ArgumentParser(
+        prog="GEM ",
+        description="This program retrieves the exchange fluxes "
+        "of a GEM model to be used in Galaxy.",
+        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."
+    )
+    args = parser.parse_args()
+
+    # Reading model from file
+    try:
+        cb_model = read_model(args.cb_model_location)
+    except Exception as e:
+        raise Exception(
+            "The model could not be read. Ensure it is in correct SBML format."
+        ) from e
+
+    # Getting exchange reactions info
+    answer = get_exchange_reactions_info(cb_model)
+
+    # Writing exchange reactions info to file
+    with open(args.out_file, "w") as outfile:
+        outfile.write(str(answer))
+
+
+if __name__ == "__main__":
+    __main__()