Merge branch 'ModelSEED:main' into main

Author: cshenry

examples/build_metabolic_model.ipynb

@@ -51,8 +51,8 @@
    ],
    "source": [
     "import cobrakbase\n",
-    "kbase = cobrakbase.KBaseAPI()\n",
-    "core_template = kbase.get_from_ws('82183/6726/1')"
+    "kbase = cobrakbase.KBaseAPI()  # or kbase = cobrakbase.KBaseAPI('YOUR_KBASE_AUTHTOKEN')\n",
+    "core_template = kbase.get_from_ws('CoreModelTemplateV3', 'NewKBaseModelTemplates')"
    ]
   },
   {

modelseedpy/fbapkg/basefbapkg.py

@@ -14,8 +14,8 @@ class FeasibilityError(Exception):
     pass
 
 #Base class for FBA packages
-class BaseFBAPkg():
-    def __init__(self,model,name,variable_types={},constraint_types={},parent = None):
+class BaseFBAPkg:
+    def __init__(self, model, name, variable_types={}, constraint_types={}, parent=None):
         self.model = model
         self.name = name
         self.childpkgs = dict()

modelseedpy/fbapkg/gapfillingpkg.py

@@ -60,10 +60,13 @@
         "rxn12006","rxn12007","rxn12014","rxn12017","rxn12022","rxn12160","rxn12161",
         "rxn01267","rxn05294","rxn04656"]
 
-#Base class for FBA packages
+
 class GapfillingPkg(BaseFBAPkg):
-    def __init__(self,model):
-        BaseFBAPkg.__init__(self,model,"gapfilling",{},{})
+    """
+
+    """
+    def __init__(self, model):
+        BaseFBAPkg.__init__(self, model, "gapfilling", {}, {})
         self.childpkgs["objective constraint"] = ObjConstPkg(model)
 
     def build_package(self,parameters):
@@ -131,9 +134,9 @@ def build_package(self,parameters):
                     if highest_score < self.parameters["reaction_scores"][rxnid][gene]:
                         highest_score = self.parameters["reaction_scores"][rxnid][gene]
                 factor = 1-0.9*highest_score
-                if "reverse" in gapfilling_penalties[reaction]:
+                if "reverse" in self.gapfilling_penalties[reaction]:
                     penalties[reaction.id]["reverse"] = factor*penalties[reaction.id]["reverse"]
-                if "forward" in gapfilling_penalties[reaction]:
+                if "forward" in self.gapfilling_penalties[reaction]:
                     penalties[reaction.id]["forward"] = factor*penalties[reaction.id]["forward"]
         self.model.solver.update()
         if self.parameters["set_objective"] == 1: