Update growth_simulation

#104 , #79
Update growth simulation + plotting model vs media (bars and heatmap)

refinegems/database/medium.py

@@ -135,7 +135,7 @@ def set_default_flux(self,flux:float =10.0, replace:bool =False, double_o2:bool
         # keep already set fluxes
         else:
             self.substance_table['flux'] = self.substance_table['flux'].fillna(flux)
-            if self.is_aerobic() and double_o2 and self.substance_table.loc[self.substance_table['name']=='Dioxygen [O2]','flux'].isna():
+            if self.is_aerobic() and double_o2 and self.substance_table.loc[self.substance_table['name']=='Dioxygen [O2]','flux'].any():
                 self.substance_table.loc[self.substance_table['name']=='Dioxygen [O2]','flux'] = 2*flux
 
     def set_oxygen_percentage(self, perc:float=1.0):

refinegems/growth.py

@@ -17,6 +17,7 @@
 import re
 from typing import Literal
 import yaml
+import matplotlib.pyplot as plt
 
 __author__ = "Famke Baeuerle and Carolin Brune"
 
@@ -261,29 +262,28 @@ def get_metabs_essential_for_growth_wrapper(model: cobraModel, media: list[mediu
 
 
 # @TEST
-def growth_sim_single(model: cobraModel, m: medium.Medium, supplement:Literal[None,'std','min'] = None, anaerobic:bool = False) -> reports.SingleGrowthSimulationReport:
+def growth_sim_single(model: cobraModel, m: medium.Medium, supplement:Literal[None,'std','min'] = None) -> reports.SingleGrowthSimulationReport:
     """Simulate the growth of a model on a given medium.
 
     Args:
         model (cobraModel): The model.
         m (medium.Medium): The medium.
         supplement (Literal[None,'std','min'], optional): Flag to add additvites to the model to ensure growth. Defaults to None (no supplements).
             Further options include 'std' for standard uptake and 'min' for minimal uptake supplementation.
-        anaerobic (bool, optional): Set medium to anaerobic/aerobic. Defaults to False (aerobic growth).
 
     Returns:
         reports.SingleGrowthSimulationReport: Object with the simulation results
     """
 
     with model:
-        # check for (an)aerobic conditions
-        if anaerobic and m.is_aerobic():
-            m.make_anaerobic()
-        if not anaerobic and not m.is_aerobic():
-            m.make_aerobic(flux=10.0)
 
         # convert to a cobrapy medium
-        exported_m = medium.medium_to_model(medium=m, model=model, add=False)
+        exported_m = medium.medium_to_model(medium=m, model=model, 
+                                            namespace='BiGG', 
+                                            default_flux=10.0, 
+                                            replace=False, 
+                                            double_o2=False, 
+                                            add=False)
 
         # supplement, if tag is set
         match supplement:
@@ -314,7 +314,6 @@ def growth_sim_single(model: cobraModel, m: medium.Medium, supplement:Literal[No
     return report
 
 
-# @TEST
 def growth_sim_multi(models: cobraModel|list[cobraModel], media: medium.Medium|list[medium.Medium], supplement_modes:list[Literal['None','min','std']]|None|Literal['None','min','std']=None) -> reports.GrowthSimulationReport:
     """Simulate the growth of (at least one) models on (at least one) media.
 
@@ -341,14 +340,14 @@ def growth_sim_multi(models: cobraModel|list[cobraModel], media: medium.Medium|l
     report = reports.GrowthSimulationReport()
     for mod in models:
         for med,supp in zip(media, supplement_modes):
-            o2_check = med.is_aerobic()
-            r = growth_sim_single(mod, med, anaerobic = not o2_check, supplement=supp)
+            r = growth_sim_single(mod, med, supplement=supp)
             report.add_sim_results(r)
 
     return report     
 
 
 # @IDEA: more options for fluxes
+# @TODO/@IDEA: validity check nefore parsing
 def read_media_config(yaml_path:str):
 
     media_list = []
@@ -436,12 +435,15 @@ def read_media_config(yaml_path:str):
     return (media_list,supplement_list)
 
 # @TODO
+# @IDEA : choose different namespaces for the media
 # main objective: read in models and media from input (command line, YAML etc.) dict?
-# -> compile a complete list media (load, add information about anaerobic, additives, fluxes and the like)
-# -> run simulation 
+# -> compile a complete list media (load, add information about anaerobic, additives, fluxes and the like) : CHECK
+# -> run simulation : CHECK
 # -> visulise also here?
 def growth_analysis(models:cobra.Model|str|list[str]|list[cobra.Model],
-                    media:medium.Medium|list[medium.Medium]|str):
+                    media:medium.Medium|list[medium.Medium]|str,
+                    supplements:None|list[Literal[None,'std','min']]=None,
+                    retrieve:Literal['report','plot','both']='plot') -> reports.GrowthSimulationReport|plt.Figure|tuple:
 
     # read-in all models into list
     # ----------------------------
@@ -452,7 +454,7 @@ def growth_analysis(models:cobra.Model|str|list[str]|list[cobra.Model],
             if len(models) > 0:
                 # if list entries are paths
                 if all(isinstance(_, str) for _ in models):
-                    mod_list = load_multiple_models(models, package='COBRApy')
+                    mod_list = load_multiple_models(models, package='cobra')
                 # if list entries are already cobra.Models
                 elif all(isinstance(_, cobra.Model) for _ in models):
                     mod_list = models
@@ -487,20 +489,26 @@ def growth_analysis(models:cobra.Model|str|list[str]|list[cobra.Model],
                 raise TypeError('Unknown type found in media, should be list fo medium.Medium.')
         # string - connection to YAML config file
         case str():
-            # @TODO
             media, supplements = read_media_config(media)
         # unknown input
         case _:
             raise ValueError(f'Unknown input for media: {media}')
 
     # run simulation
     # --------------
-    report = growth_sim_multi(models, media)
-
-    return report
+    report = growth_sim_multi(mod_list, media, supplements)
 
     # save / visualise report 
-    pass
+    # -----------------------
+    match retrieve:
+        case 'report':
+            return report
+        case 'plot':
+            return report.plot_growth()
+        case 'both':
+            return (report, report.plot_growth)
+        case _:
+            raise ValueError(f'Unknown input for retrieve: {retrieve}')
 
 
 # @RENAMED

refinegems/io.py

@@ -23,7 +23,7 @@
 from libsbml import Model as libModel
 from libsbml import SBMLReader, writeSBMLToFile, SBMLValidator, SBMLDocument
 from datetime import date
-from typing import Union
+from typing import Union, Literal
 
 __author__ = "Tobias Fehrenbach, Famke Baeuerle and Gwendolyn O. Döbel"
 
@@ -56,12 +56,12 @@ def load_model_libsbml(modelpath: str) -> libModel:
     return mod
 
 
-def load_multiple_models(models: list[str], package: str) -> list:
+def load_multiple_models(models: list[str], package: Literal['cobra','libsbml']) -> list:
     """Loads multiple models into a list
 
     Args:
         - models (list): List of paths to models
-        - package (str): COBRApy|libSBML
+        - package (str): cobra|libsbml
 
     Returns:
         list: List of model objects loaded with COBRApy|libSBML

refinegems/media_config.yml

@@ -32,13 +32,15 @@ media:
     aerobic: False
   LB_o2:
     base: LB
+    default_flux: 5.0
+    o2_percent: 2.0
   SNM3:
-    supplement: min
+#    supplement: min
   M9:
-    add: 
-      - aa
-      - SNM3
-  PERS:
-    external_base: link
-    add_external:
-      - link
+#    add: 
+#      - aa
+#      - SNM3
+#  PERS:
+#    external_base: link
+#    add_external:
+#      - link