feat(rpfba): add outfile name of rpfba merged model

brsynth · Nov 20, 2023 · cbf7e86 · cbf7e86
1 parent 638031a
commit cbf7e86
Show file tree

Hide file tree

Showing 3 changed files with 8 additions and 9 deletions.
diff --git a/rptools/rpfba/Args.py b/rptools/rpfba/Args.py
@@ -43,8 +43,8 @@ def add_arguments(parser: ArgumentParser):
     )
     parser.add_argument(
         "--merge",
-        action="store_true",
-        default=False,
+        type=str,
+        default="",
         help="output the full merged model in addition of heterologous pathway only (default: False)",
     )
     parser.add_argument(

diff --git a/rptools/rpfba/rpfba.py b/rptools/rpfba/rpfba.py
@@ -67,12 +67,12 @@ def preprocess(
     if args.ignore_orphan_species:
         merged_model.search_isolated_species(missing_species)
 
-    if args.merge:
-        merged_outfile = (
-            pathway.get_id() + "__MERGED_IN__" + model.getName() + ".sbml"
-        )
-        logger.info(f"Write merged rpSBML file to {merged_outfile}")
-        merged_model.write_to_file(merged_outfile)
+    if args.merge != "":
+        # merged_outfile = (
+        #     pathway.get_id() + "__MERGED_IN__" + model.getName() + ".sbml"
+        # )
+        logger.info(f"Write merged rpSBML file to {args.merge}")
+        merged_model.write_to_file(args.merge)
 
     return merged_model, pathway, ids
 

diff --git a/rptools/rpviz/Viewer.py b/rptools/rpviz/Viewer.py
@@ -7,7 +7,6 @@
 __license__ = 'MIT'
 
 
-import os
 import pandas
 import distutils.dir_util
 from pathlib import Path