FileNotFoundError: Missing bigg_reactions.tsv when using dbType='BiGG'

[WXG920713]

gapfiller_result_complete = dnngior.Gapfill(
draftModel=draft_model_path,
medium=None,
objectiveName=biomass_objective_id,
dbType='BiGG'
)

Gap-filling database = BiGG
No objective coefficients in model. Unclear what should be optimized

FileNotFoundError Traceback (most recent call last)
Cell In[34], line 2

----> 2 gapfiller_result_complete = dnngior.Gapfill(
3 draftModel=draft_model_path,
4 medium=None,
5 objectiveName=biomass_objective_id,
6 dbType='BiGG'
7 )
8 print("Gap-filling with complete medium finished (BiGG model).")

File /usr/local/Caskroom/miniforge/base/envs/dnngior/lib/python3.9/site-packages/dnngior/gapfill_class.py:70, in Gapfill.init(self, draftModel, trainedNNPath, medium, medium_file, black_list, grey_list, punish_cost, default_cost, objectiveName, dbType, gapfill)
67 # Build a Reaction object for the exchange reactions;
68 # if you have a defined medium, set the fixed_bounds argument accordingly
69 self.exchange_reacs = Reaction(model = self.path_to_exchanges, fixed_bounds = self.medium)
---> 70 self.db_reactions = Reaction(biochem_input = self.path_to_biochem, dbType=self.dbType)
72 # Merge reactions from db with those of the draft model
73 self.all_reactions = Reaction(fixed_bounds = self.medium, dbType=self.dbType)

File /usr/local/Caskroom/miniforge/base/envs/dnngior/lib/python3.9/site-packages/dnngior/reaction_class.py:63, in Reaction.init(self, model_folder, model_list, model, biochem_input, dbType, fixed_bounds)
59 self.model = self.__get_model(model)
61 self.dbType = dbType
---> 63 self.biochem_input = self.__get_reactions_from_biochem_input(biochem_input)
65 self.reactions = self.__get_reactions()

File /usr/local/Caskroom/miniforge/base/envs/dnngior/lib/python3.9/site-packages/dnngior/reaction_class.py:112, in Reaction.__get_reactions_from_biochem_input(self, biochem_input)
109 if biochem_input is None:
110 return None
--> 112 react_d = self.read_biochemistry_table(biochem_input)
113 reactions = {}
114 for reaction in react_d:
115
116 #I am assuming bacterial models (c0 and e0 compartments) and modelSEED identifiers
117 #as 'rxn00001'

File /usr/local/Caskroom/miniforge/base/envs/dnngior/lib/python3.9/site-packages/dnngior/reaction_class.py:323, in Reaction.read_biochemistry_table(self, filePath)
317 """
318 Reads a ModelSEED/PATRIC reaction database table, using the id, stoichiometry, direction and equation columns.
319 Returns a dictionary where id maps to a list of the other columns.
320 """
321 biochem = {}
--> 323 with open(filePath, 'r') as f:
324 f.readline() #Skip the header
325 for line in f:

FileNotFoundError: [Errno 2] No such file or directory: '/usr/local/Caskroom/miniforge/base/envs/dnngior/lib/python3.9/site-packages/dnngior/files/biochemistry/bigg_reactions.tsv'

[Biomerene]

The database for BiGG was accidentally left out of the package. You could fix this manually by getting it from the docs folder of the git here, and placing it in you local install installation of your package: /usr/local/Caskroom/miniforge/base/envs/dnngior/lib/python3.9/site-packages/dnngior/files/biochemistry/. It will be fixed in future versions, my apologies for the inconvenience.