More comments and statistics

Author: Paulocracy

cva_vars_aerobic_OPTMDF_0,818_STANDARDCONC.txt renamed to cosa/cva_vars_aerobic_OPTMDF_0,818_STANDARDCONC.txt

@@ -1,15 +1,15 @@
-from tkinter.messagebox import NO
-import matplotlib.pyplot as plt
+"""This module contains the function for the Concentration Variability Analysis (CVA)."""
+
+# IMPORT SECTION #
+# External
 import cobra
 import copy
+import matplotlib.pyplot as plt
 import os
 import pulp
 from math import exp
-from cosa_get_all_tcosa_reaction_ids import get_all_tcosa_reaction_ids
-from cosa_get_model_with_nadx_scenario import cosa_get_model_with_nadx_scenario
-from cosa_get_suffix import cosa_get_suffix
-from helper import json_load, json_write, json_zip_load
-from typing import List
+from typing import Dict, List
+# Internal
 from optmdfpathway import (
     STANDARD_R, STANDARD_T, get_optmdfpathway_base_problem,
     add_differential_reactions_constraints, get_z_variable_status,
@@ -18,11 +18,24 @@
 from cosa_load_model_data import (
     MIN_OPTMDF, load_model_data
 )
-from typing import Dict
-from helper import ensure_folder_existence
+from cosa_get_all_tcosa_reaction_ids import get_all_tcosa_reaction_ids
+from cosa_get_model_with_nadx_scenario import cosa_get_model_with_nadx_scenario
+from cosa_get_suffix import cosa_get_suffix
+from helper import ensure_folder_existence, json_load, json_write, json_zip_load
 
 
+# PUBLIC FUNCTIONS SECTION #
 def cosa_cva(metabolites: List[str], anaerobic: bool, expanded: bool, growth_epsilon: float = 0.01) -> None:
+    """Performs a concentration variability analysis (CVA).
+
+    As a results, it writes JSON files with the CVA results in the 'cosa' subfolder'
+
+    ### Arguments
+    * metabolites: List[str] ~ List of metabolite IDs for all metabolites for which a CVA shall be performed.
+    * anaerobic: bool ~ Whether or not anaerobicity is the case.
+    * expanded: bool ~ Whether (True) 3 or 2 (False) redox cofactors are used.
+    * growth_epsilon: float = 0.01 ~ The numeric stability factor to go below µ.
+    """
     suffix = cosa_get_suffix(anaerobic, expanded)
     figures_path = f"./cosa/results{suffix}/figures/"
     ensure_folder_existence(figures_path)

cva_vars_aerobic_OPTSUBMDF_0,818_STANDARDCONC.txt renamed to cosa/cva_vars_aerobic_OPTSUBMDF_0,818_STANDARDCONC.txt

@@ -1,11 +1,13 @@
+"""This module produces a text file with some CVA variability statistics."""
+
 from helper import json_load
 
 top = 15
 used_mu = "0,818"
 
 for aerobicity in ("aerobic",):
     for target in ("OPTMDF", "OPTSUBMDF"):
-        txtpath = f"cva_vars_{aerobicity}_{target}_{used_mu}_STANDARDCONC.txt"
+        txtpath = f"./cosa/cva_vars_{aerobicity}_{target}_{used_mu}_STANDARDCONC.txt"
         jsondata = json_load(f"./cosa/results_{aerobicity}/cva_{target}_STANDARDCONC.json")
 
         num_not_max_var = 0
@@ -47,4 +49,3 @@
 
         with open(txtpath, "w", encoding="utf-8") as f:
             f.write(txt)
-

cosa_cva.py

@@ -1,3 +1,4 @@
+"""Performs the dGf sampling under aerobic conditions."""
 from cosa_dG0_sampling import cosa_dG0_sampling
 from cosa_random_sampling_figures import create_cosa_dG0_sampling_figures, create_total_dG0_sampling_figure
 

cosa_cva_variability_statistics.py

@@ -1,3 +1,4 @@
+"""Performs the dGf sampling under anaerobic conditions."""
 from cosa_dG0_sampling import cosa_dG0_sampling
 from cosa_random_sampling_figures import create_cosa_dG0_sampling_figures, create_total_dG0_sampling_figure
 

cosa_dG0_sampling_aerobic.py

@@ -1,3 +1,5 @@
+"""Performs a thermodynamic FVA under the given settings. See 'cosa_fva_aerobic' and 'cosa_fva_anaerobic' for its application."""
+
 import cobra
 import copy
 import os

cosa_dG0_sampling_anaerobic.py

@@ -1,11 +1,16 @@
+"""This modules creates the Supplementary Table 3."""
+
+# IMPORT SECTION #
+# External
 import copy
 import math
 import openpyxl
-from helper import json_load
+# Internal
 from cosa_load_model_data import load_model_data
 from cosa_get_model_with_nadx_scenario import cosa_get_model_with_nadx_scenario
+from helper import json_load
 
-
+# LOGIC SECTION #
 core_ids = [
     "EX_glc__D_e",
     "GLCptspp",