Fix some bugs, primarily addressing issue #3

klamt-lab · Jul 27, 2020 · 30d3807 · 30d3807
1 parent 8a2fec5
commit 30d3807
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Showing 4 changed files with 12 additions and 7 deletions.
diff --git a/autopacmen/submodules/get_initial_spreadsheets.py b/autopacmen/submodules/get_initial_spreadsheets.py
@@ -248,7 +248,7 @@ def get_initial_spreadsheets(model: cobra.Model, project_folder: str, project_na
     worksheet.write(1, 0, "Fraction of masses of model-included enzymes in comparison to all enzymes (0.0 to 1.0):")
     worksheet.write(1, 1, 1.0)
     worksheet.write(2, 0, "Average saturation level (0.0 to 1.0):")
-    worksheet.write(2, 0, 1.0)
+    worksheet.write(2, 1, 1.0)
     worksheet2 = workbook.add_worksheet("Single protein data")
     worksheet2.write(0, 0, "Protein ID (as in SBML model)")
     worksheet2.write(0, 1, "Protein concentration [mmol/gDW]")

diff --git a/autopacmen/submodules/get_reactions_kcat_mapping.py b/autopacmen/submodules/get_reactions_kcat_mapping.py
@@ -127,7 +127,7 @@ def _get_kcat_list(searched_metabolites: List[str], complete_entry: Dict[str, An
     species_to_search: List[str] = []
     taxonomy_dict_cache: Dict[str, List[str]] = {}
     for species in all_species:
-        cache_filename = species + "_taxonomy"
+        cache_filename = species.replace("/", "") + "_taxonomy"
         if cache_filename in cache_files:
             cache_filepath = cache_basepath + cache_filename
             taxonomy_dict_cache[species] = pickle_load(cache_filepath)
@@ -149,7 +149,7 @@ def _get_kcat_list(searched_metabolites: List[str], complete_entry: Dict[str, An
                 taxonomy_dict_search[searched_species] = ["NOT FOUND"]
 
         for species in list(taxonomy_dict_search.keys()):
-            cache_filename = species + "_taxonomy"
+            cache_filename = species.replace("/", "") + "_taxonomy"
             if taxonomy_dict_search[species] == ["NOT FOUND"]:
                 cache_filename += "_NA"
             cache_filepath = cache_basepath + cache_filename

diff --git a/autopacmen/submodules/parse_brenda_textfile.py b/autopacmen/submodules/parse_brenda_textfile.py
@@ -142,9 +142,14 @@ def parse_brenda_textfile(brenda_textfile_path: str, bigg_metabolites_json_folde
     for ec_number in ec_numbers:
         if "(transferred to " in ec_number:
             actual_ec_number = ec_number.split(" (transferred")[0]
-            brenda_kcat_database[actual_ec_number] = {}
-            brenda_kcat_database[actual_ec_number]["TRANSFER"] = \
-                ec_number.lower().split("(transferred to ec")[1].replace(")", "").lstrip()
+            try:
+                brenda_kcat_database[actual_ec_number] = {}
+                brenda_kcat_database[actual_ec_number]["TRANSFER"] = \
+                    ec_number.lower().replace("  ", " ").split("(transferred to ec")[1].replace(")", "").lstrip()
+            except Exception:
+                # Some transfers go to general subgroups instead of single EC numbers so that
+                # no kcat database can be built from it D:
+                print("WARNING: BRENDA text file line " + ec_number + " is not interpretable!")
             continue
 
         brenda_kcat_database[ec_number] = {}

diff --git a/setup.py b/setup.py
@@ -5,7 +5,7 @@
 
 setuptools.setup(
     name="autopacmen-Paulocracy",
-    version="0.5.4",
+    version="0.5.5",
     author="Paulocracy",
     author_email="bekiaris@mpi-magdeburg.mpg.de",
     description="The AutoPACMEN package",