diff --git a/autopacmen/submodules/get_initial_spreadsheets.py b/autopacmen/submodules/get_initial_spreadsheets.py index 3c74003..ec8976f 100644 --- 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 index 6acad0f..1a5c5a3 100644 --- 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 index 527396c..9cb8183 100644 --- 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 index f610337..d10f2bd 100644 --- 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",