Prepare new FVA runs

Author: Paulocracy

cosa/total_dG0_sampling_figure_change_range_10_STANDARDCONC.png

@@ -115,15 +115,12 @@ def cosa_single_swap_test(anaerobic : bool, reac_id: str, mu: float, base_nadx_s
 
     suffix = cosa_get_suffix(anaerobic, expanded=False, c_source=c_source)
 
-    # figures_path = f"./cosa/results{suffix}/figures/"
-    # ensure_folder_existence(figures_path)
-
     report = ""
     original_cobra_model = copy.deepcopy(cobra_model)
     for concentrations in ("STANDARDCONCS", "PAPERCONCS"):
         output_filepath = f"./cosa/variability_{suffix}_{reac_id}_{concentrations}_{base_nadx_scenario}.json"
-        if os.path.exists(output_filepath):
-            continue
+        # if os.path.exists(output_filepath):
+        #     continue
 
         print(f"=CONCENTRATION RANGES: {concentrations}=")
         report += f"=CONCENTRATION RANGES: {concentrations}=\n"
@@ -162,6 +159,15 @@ def cosa_single_swap_test(anaerobic : bool, reac_id: str, mu: float, base_nadx_s
                     tested_vars.append(reaction.id)
         tested_vars = list(set(tested_vars))
 
+        variable_ids = list(optmdfpathway_base_variables.keys())
+        f_var_addition = []
+        for tested_var in tested_vars:
+            f_var = f"f_var_{tested_var}"
+            if f_var in variable_ids:
+                f_var_addition.append(f_var)
+        tested_vars += f_var_addition
+        tested_vars += ["var_B", "var_B2"]
+
         # tested_vars = [f"f_var_{x}" for x in get_all_tcosa_reaction_ids(cobra_model)] + get_all_tcosa_reaction_ids(cobra_model)
         # tested_vars = [x for x in tested_vars if ((("_ORIGINAL_") in x) or (("_VARIANT_") in x)) and (x in optmdf_result["values"].keys())]
         # tested_vars += ["x_nad_tcosa_c", "x_nadp_tcosa_c", "x_nadh_tcosa_c", "x_nadph_tcosa_c"]
@@ -179,10 +185,7 @@ def cosa_single_swap_test(anaerobic : bool, reac_id: str, mu: float, base_nadx_s
             1e12,
         )
         print(optmdf_result["values"]["var_B"])
-        # fva_results["OptMDF"] = perform_variability_analysis(
-        #     tested_vars=tested_vars,
-        #     base_problem=optmdfpathway_base_problem,
-        # )
+
         fva_results["OptMDF"] = perform_fva_multi(
             var_ids=tested_vars,
             base_problem=optmdfpathway_base_problem,

cosa/total_dG0_sampling_figure_change_range_15_STANDARDCONC.png

@@ -4,13 +4,13 @@
 import ray
 ray.init(log_to_driver=False)
 
-for base_nadx_scenario in ("WILDTYPE", "FLEXIBLE"):
-    cosa_single_swap_test(
-        anaerobic=False,
-        reac_id="TEST_0_868",
-        mu=0.868,
-        base_nadx_scenario=base_nadx_scenario
-    )
+for base_nadx_scenario in ("WILDTYPE", "FLEXIBLE", "SINGLE_COFACTOR"):
+    # cosa_single_swap_test(
+    #     anaerobic=False,
+    #     reac_id="TEST_0_868",
+    #     mu=0.868,
+    #     base_nadx_scenario=base_nadx_scenario
+    # )
     cosa_single_swap_test(
         anaerobic=False,
         reac_id="TEST_0_818",
@@ -29,12 +29,12 @@
     #     mu=0.718,
     #     base_nadx_scenario=base_nadx_scenario
     # )
-    cosa_single_swap_test(
-        anaerobic=False,
-        reac_id="TEST_0_668",
-        mu=0.668,
-        base_nadx_scenario=base_nadx_scenario
-    )
+    # cosa_single_swap_test(
+    #     anaerobic=False,
+    #     reac_id="TEST_0_668",
+    #     mu=0.668,
+    #     base_nadx_scenario=base_nadx_scenario
+    # )
     # cosa_single_swap_test(
     #     anaerobic=False,
     #     reac_id="TEST_0_618",
@@ -59,12 +59,12 @@
     #     mu=0.468,
     #     base_nadx_scenario=base_nadx_scenario
     # )
-    cosa_single_swap_test(
-        anaerobic=False,
-        reac_id="TEST_0_418",
-        mu=0.418,
-        base_nadx_scenario=base_nadx_scenario
-    )
+    # cosa_single_swap_test(
+    #     anaerobic=False,
+    #     reac_id="TEST_0_418",
+    #     mu=0.418,
+    #     base_nadx_scenario=base_nadx_scenario
+    # )
     # cosa_single_swap_test(
     #     anaerobic=False,
     #     reac_id="TEST_0_368",
@@ -95,12 +95,12 @@
     #     mu=0.268,
     #     base_nadx_scenario=base_nadx_scenario
     # )
-    cosa_single_swap_test(
-        anaerobic=False,
-        reac_id="TEST_0_218",
-        mu=0.218,
-        base_nadx_scenario=base_nadx_scenario
-    )
+    # cosa_single_swap_test(
+    #     anaerobic=False,
+    #     reac_id="TEST_0_218",
+    #     mu=0.218,
+    #     base_nadx_scenario=base_nadx_scenario
+    # )
     # cosa_single_swap_test(
     #     anaerobic=False,
     #     reac_id="TEST_0_168",
@@ -119,12 +119,12 @@
     #     mu=0.068,
     #     base_nadx_scenario=base_nadx_scenario
     # )
-    cosa_single_swap_test(
-        anaerobic=False,
-        reac_id="TEST_0_05",
-        mu=0.05,
-        base_nadx_scenario=base_nadx_scenario
-    )
+    # cosa_single_swap_test(
+    #     anaerobic=False,
+    #     reac_id="TEST_0_05",
+    #     mu=0.05,
+    #     base_nadx_scenario=base_nadx_scenario
+    # )
     # cosa_single_swap_test(
     #     anaerobic=False,
     #     reac_id="TEST_0_03",

cosa/total_dG0_sampling_figure_change_range_20_STANDARDCONC.png

@@ -4,39 +4,39 @@
 import ray
 ray.init(log_to_driver=False)
 
-for base_nadx_scenario in ("WILDTYPE", "FLEXIBLE"):
-    cosa_single_swap_test(
-        anaerobic=False,
-        reac_id="TEST_0_206",
-        mu=0.2059,
-        base_nadx_scenario=base_nadx_scenario,
-        c_source="acetate",
-    )
+for base_nadx_scenario in ("WILDTYPE", "FLEXIBLE", "SINGLE_COFACTOR"):
+    # cosa_single_swap_test(
+    #     anaerobic=False,
+    #     reac_id="TEST_0_206",
+    #     mu=0.2059,
+    #     base_nadx_scenario=base_nadx_scenario,
+    #     c_source="acetate",
+    # )
     cosa_single_swap_test(
         anaerobic=False,
         reac_id="TEST_0_156",
         mu=0.156,
         base_nadx_scenario=base_nadx_scenario,
         c_source="acetate",
     )
-    cosa_single_swap_test(
-        anaerobic=False,
-        reac_id="TEST_0_106",
-        mu=0.106,
-        base_nadx_scenario=base_nadx_scenario,
-        c_source="acetate",
-    )
-    cosa_single_swap_test(
-        anaerobic=False,
-        reac_id="TEST_0_056",
-        mu=0.056,
-        base_nadx_scenario=base_nadx_scenario,
-        c_source="acetate",
-    )
-    cosa_single_swap_test(
-        anaerobic=False,
-        reac_id="TEST_0_003",
-        mu=0.03,
-        base_nadx_scenario=base_nadx_scenario,
-        c_source="acetate",
-    )
+    # cosa_single_swap_test(
+    #     anaerobic=False,
+    #     reac_id="TEST_0_106",
+    #     mu=0.106,
+    #     base_nadx_scenario=base_nadx_scenario,
+    #     c_source="acetate",
+    # )
+    # cosa_single_swap_test(
+    #     anaerobic=False,
+    #     reac_id="TEST_0_056",
+    #     mu=0.056,
+    #     base_nadx_scenario=base_nadx_scenario,
+    #     c_source="acetate",
+    # )
+    # cosa_single_swap_test(
+    #     anaerobic=False,
+    #     reac_id="TEST_0_003",
+    #     mu=0.03,
+    #     base_nadx_scenario=base_nadx_scenario,
+    #     c_source="acetate",
+    # )

cosa/variability__aerobic_TEST_0_03_STANDARDCONCS_WILDTYPE.json

@@ -5,13 +5,13 @@
 ray.init(log_to_driver=False)
 
 
-for base_nadx_scenario in ("FLEXIBLE",): #("WILDTYPE", "FLEXIBLE"):
-    cosa_single_swap_test(
-        anaerobic=True,
-        reac_id="TEST_0_371",
-        mu=0.371,
-        base_nadx_scenario=base_nadx_scenario
-    )
+for base_nadx_scenario in ("WILDTYPE", "FLEXIBLE", "SINGLE_COFACTOR"):
+    # cosa_single_swap_test(
+    #     anaerobic=True,
+    #     reac_id="TEST_0_371",
+    #     mu=0.371,
+    #     base_nadx_scenario=base_nadx_scenario
+    # )
     cosa_single_swap_test(
         anaerobic=True,
         reac_id="TEST_0_321",
@@ -30,12 +30,12 @@
     #     mu=0.221,
     #     base_nadx_scenario=base_nadx_scenario
     # )
-    cosa_single_swap_test(
-        anaerobic=True,
-        reac_id="TEST_0_171",
-        mu=0.171,
-        base_nadx_scenario=base_nadx_scenario
-    )
+    # cosa_single_swap_test(
+    #     anaerobic=True,
+    #     reac_id="TEST_0_171",
+    #     mu=0.171,
+    #     base_nadx_scenario=base_nadx_scenario
+    # )
     # cosa_single_swap_test(
     #     anaerobic=True,
     #     reac_id="TEST_0_121",
@@ -48,12 +48,12 @@
     #     mu=0.071,
     #     base_nadx_scenario=base_nadx_scenario
     # )
-    cosa_single_swap_test(
-        anaerobic=True,
-        reac_id="TEST_0_05",
-        mu=0.05,
-        base_nadx_scenario=base_nadx_scenario
-    )
+    # cosa_single_swap_test(
+    #     anaerobic=True,
+    #     reac_id="TEST_0_05",
+    #     mu=0.05,
+    #     base_nadx_scenario=base_nadx_scenario
+    # )
     # cosa_single_swap_test(
     #     anaerobic=True,
     #     reac_id="TEST_0_03",