changeset 325:7cf50f1de512 draft

Uploaded

--- a/marea_2/custom_data_generator.py	Mon Aug 05 14:37:21 2024 +0000
+++ b/marea_2/custom_data_generator.py	Mon Aug 05 19:22:26 2024 +0000
@@ -30,14 +30,18 @@
     parser.add_argument("-mn", "--name",    type = str, required = True, help = "Input model name")
     # ^ I need this because galaxy converts my files into .dat but I need to know what extension they were in
 
-    parser.add_argument(
-        "-of", "--output_format",
-        # vvv I have to use .fromExt because enums in python are the plague and have been implemented by a chimpanzee.
-        type = utils.FileFormat.fromExt, default = utils.FileFormat.PICKLE,
-        choices = [utils.FileFormat.CSV, utils.FileFormat.PICKLE],
-        # ^^^ Not all variants are valid here, otherwise list(utils.FileFormat) would be best.
-        required = True, help = "Extension of all output files")
-    
+    parser.add_argument('-bounds', '--bounds',
+                    type = str,
+                    help = 'output of bounds tsv')
+    parser.add_argument('-reactions', '--reactions',
+                type = str,
+                help = 'output of reactions tsv')
+    parser.add_argument('-medium', '--medium',
+                type = str,
+                help = 'output of medium tsv')
+    parser.add_argument('-rules', '--rules',
+                type = str,
+                help = 'output of rules tsv')
     argsNamespace = parser.parse_args()
     argsNamespace.out_dir = "result"
     # ^ can't get this one to work from xml, there doesn't seem to be a way to get the directory attribute from the collection
@@ -160,7 +164,7 @@
         None
     """
     with open(file_path.show(), 'w', newline='') as csvfile:
-        writer = csv.DictWriter(csvfile, fieldnames = fieldNames)
+        writer = csv.DictWriter(csvfile, fieldnames = fieldNames, delimiter='\t')
         writer.writeheader()
 
         for key, value in data.items():
@@ -185,6 +189,8 @@
     model = load_custom_model(
         utils.FilePath.fromStrPath(ARGS.input), utils.FilePath.fromStrPath(ARGS.name).ext)
     
+    ARGS.output_format = utils.FileFormat.CSV
+    
     # generate data and save it in the desired format and in a location galaxy understands
     # (it should show up as a collection in the history)
     rulesPath     = utils.FilePath("rules",     ARGS.output_format, prefix = ARGS.out_dir)
@@ -209,10 +215,10 @@
         reactions = generate_reactions(model, asParsed = False)
         bounds = generate_bounds(model)
         medium = get_medium(model)
-        save_as_csv(rules,     rulesPath,     ("ReactionID", "Rule"))
-        save_as_csv(reactions, reactionsPath, ("ReactionID", "Reaction"))
-        bounds.to_csv(boundsPath.show())
-        medium.to_csv(mediumPath.show())
+        save_as_csv(rules,     ARGS.rules,     ("ReactionID", "Rule"))
+        save_as_csv(reactions, ARGS.reactions, ("ReactionID", "Reaction"))
+        bounds.to_csv(ARGS.bounds)
+        medium.to_csv(ARGS.medium)
 
 
     # ^ Please if anyone works on this after updating python to 3.12 change the if/elif into a match statement!!