commscores edits

modelseedpy/community/commhelper.py

@@ -28,13 +28,14 @@ def correct_nonMSID(nonMSobject, output, model_index):
     name, compartment = output
     index = 0 if compartment == "e" else model_index
     nonMSobject.compartment = compartment + str(index)
-    comp = re.search(r"(_\w\d+$)", nonMSobject.id)
-    if comp is None:  return nonMSobject.id.replace(rf"[{compartment}]", f"_{nonMSobject.compartment}")
+    comp = re.search(r"(_[a-z]\d+$)", nonMSobject.id)
+    if comp is None and rf"[{compartment}]" in nonMSobject.id:  return nonMSobject.id.replace(rf"[{compartment}]", f"_{nonMSobject.compartment}")
+    elif comp is None:  return nonMSobject.id + f"_{nonMSobject.compartment}"
     return "_".join([nonMSobject.id.replace(comp.group(), ""), nonMSobject.compartment])
 
 
 def build_from_species_models(org_models, model_id=None, name=None, abundances=None,
-                              standardize=False, copy_models=True, printing=False):
+                              standardize=False, MSmodel = True, copy_models=True, printing=False):
     """Merges the input list of single species metabolic models into a community metabolic model
 
     Parameters
@@ -65,6 +66,7 @@ def build_from_species_models(org_models, model_id=None, name=None, abundances=N
         model_util = MSModelUtil(org_model, copy=copy_models)
         model_reaction_ids = [rxn.id for rxn in model_util.model.reactions]
         model_index += 1
+        # if MSmodel:
         # Rename metabolites
         for met in model_util.model.metabolites:
             # Renaming compartments
@@ -112,8 +114,7 @@ def build_from_species_models(org_models, model_id=None, name=None, abundances=N
                     output = MSModelUtil.parse_id(rxn)
                     if output is None:
                         if printing:  print(f"The {rxn.id} ({output}; {hasattr(rxn, 'compartment')}) is unpredictable.")
-                        try:
-                            rxn.id = correct_nonMSID(rxn, (rxn.id, "c"), model_index)
+                        try:   rxn.id = correct_nonMSID(rxn, (rxn.id, "c"), model_index)
                         except ValueError: pass
                     elif len(output) == 2:  rxn.id = correct_nonMSID(rxn, output, model_index)
                     elif len(output) == 3:
@@ -128,6 +129,9 @@ def build_from_species_models(org_models, model_id=None, name=None, abundances=N
                     if string_diff and not all(FBAHelper.isnumber(x) for x in string_diff):
                         print(f"The ID {initialID} is changed with {string_diff} to create the final ID {finalID}")
             new_reactions.add(rxn)
+        # else:
+        #     # TODO develop a method for compartmentalizing models without editing all reaction IDs or assuming their syntax
+        #     pass
     # adds only unique reactions and metabolites to the community model
     newmodel = Model(model_id or "+".join([model.id for model in models]),
                      name or "+".join([model.name for model in models]))

modelseedpy/community/mscommunity.py

@@ -103,7 +103,7 @@ def __init__(self, model=None, member_models: list = None, ids=None, abundances=
         if "cpd11416" not in msid_cobraid_hash:  raise KeyError("Could not find biomass compound for the model.")
         other_biomass_cpds = []
         for self.biomass_cpd in msid_cobraid_hash["cpd11416"]:
-            if self.biomass_cpd.compartment == "c0":
+            if "c" in self.biomass_cpd.compartment:
                 for rxn in self.util.model.reactions:
                     if self.biomass_cpd not in rxn.metabolites:  continue
                     print(self.biomass_cpd, rxn, end=";\t")

modelseedpy/core/msminimalmedia.py

@@ -36,7 +36,7 @@ def _var_to_ID(var):
 
 
 def _compatibilize(org_models, printing=False):
-from commscores import GEMCompatibility
+    from commscores import GEMCompatibility
     return GEMCompatibility.standardize(org_models, conflicts_file_name="standardization_corrections.json", printing=printing)
 
 
@@ -61,7 +61,7 @@ def minimizeFlux_withGrowth(model_util, min_growth, obj):
     model_util.add_objective(obj, "min")
     # print(model_util.model.objective)
     # print([(cons.lb, cons.expression) for cons in model_util.model.constraints if "min" in cons.name])
-    sol = model_util.model.optimize()
+    sol = model_util.model.optimize()   
     # print(sol.objective_value)
     sol_dict = bioFlux_check(model_util.model, sol, min_growth=min_growth)
     return sol, sol_dict