commscores community updates

freiburgermsu · Dec 7, 2023 · 2d81a53 · 2d81a53
1 parent 249af79
commit 2d81a53
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Showing 2 changed files with 9 additions and 7 deletions.
diff --git a/modelseedpy/community/commhelper.py b/modelseedpy/community/commhelper.py
@@ -125,9 +125,10 @@ def build_from_species_models(org_models, model_id=None, name=None, abundances=N
                             if index == "":  rxn.id += str(model_index)
                             else:  rxn.id = rxn_id + str(model_index)
                     finalID = str(rxn.id)
-                    string_diff = set(initialID).symmetric_difference(set(finalID))
-                    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}")
+                    string_diff = ""
+                    for index, let in enumerate(finalID):
+                        if index >= len(initialID) or index < len(initialID) and let != initialID[index]: string_diff += let
+                    if string_diff != f"_{compartment}{model_index}":  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

diff --git a/modelseedpy/community/mscommunity.py b/modelseedpy/community/mscommunity.py
@@ -8,13 +8,13 @@
 from modelseedpy.core.fbahelper import FBAHelper
 #from modelseedpy.fbapkg.gapfillingpkg import default_blacklist
 from modelseedpy.core.msatpcorrection import MSATPCorrection
-from cobra import Reaction
+from cobra.io import save_matlab_model, write_sbml_model
 from cobra.core.dictlist import DictList
-from cobra.io import save_matlab_model
 from optlang.symbolics import Zero
 from optlang import Constraint
 from pandas import DataFrame
 from pprint import pprint
+from cobra import Reaction
 import logging
 
 logger = logging.getLogger(__name__)
@@ -97,13 +97,14 @@ def __init__(self, model=None, member_models: list = None, ids=None, abundances=
         self.pkgmgr = MSPackageManager.get_pkg_mgr(self.util.model)
         msid_cobraid_hash = self.util.msid_hash()
         # print(msid_cobraid_hash)
+        write_sbml_model(model, "test_comm.xml")
 
         # TODO this logic needs to be updated to accommodate non-MS models
 
         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 "c" in self.biomass_cpd.compartment:
+            if "c0" in self.biomass_cpd.id:
                 for rxn in self.util.model.reactions:
                     if self.biomass_cpd not in rxn.metabolites:  continue
                     print(self.biomass_cpd, rxn, end=";\t")
@@ -114,7 +115,7 @@ def __init__(self, model=None, member_models: list = None, ids=None, abundances=
                         if printing:  print('primary biomass defined', rxn.id)
                         self.primary_biomass = rxn
                     elif rxn.metabolites[self.biomass_cpd] < 0 and len(rxn.metabolites) == 1:  self.biomass_drain = rxn
-            elif 'c' in self.biomass_cpd.compartment:  # TODO expand to capture nonMS models
+            elif 'c' in self.biomass_cpd.compartment:
                 other_biomass_cpds.append(self.biomass_cpd)
         # assign community members and their abundances
         abundances = abundances or [1/len(other_biomass_cpds)]*len(other_biomass_cpds)