Enhanced applicability of the polish.py module #36 #46

1. Changed parameters in `config.yaml`:
- Renamed parameter `polish_carveme` to `polish`
- Added parameter `BiGG_IDs`
2. Changed `main.py` according to 'new' parameters

config.yaml

@@ -21,8 +21,9 @@ kegg_path:  '../C_striatum_GEMs/models/Cstr_KC-Na-01.xml' # path where to save m
 sboterms: FALSE
 sbo_path: '../C_striatum_GEMs/models/Cstr_KC-Na-01.xml' # path where to save model with sbo terms
 
-### CarveMe polishing ###
-polish_carveme: FALSE
+### Model polishing ### If model has no BiGG IDs, set parameter BiGG_IDs to FALSE
+polish: FALSE
+BiGG_IDs: TRUE
 polish_path: '../C_striatum_GEMs/models/Cstr_KC-Na-01.xml' # path where to save the polished model
 
 ### Charge correction ###

main.py

@@ -29,9 +29,12 @@ def main():
         model, errors = cobra.io.sbml.validate_sbml_model(config['sbo_path'])
         print(errors)
 
-    elif (config['polish_carveme']):
+    elif (config['polish']):
         model_libsbml = rg.load.load_model_libsbml(config['model'])
-        rg.polish.polish_carveme_bigg(model_libsbml, config['polish_path'], config['entrez_email'])
+        if config['BiGG_IDs']:
+           rg.polish.polish_carveme_bigg(model_libsbml, config['polish_path'], config['entrez_email'])
+        else:
+         rg.polish.polish_not_bigg(model_libsbml, config['polish_path'], config['entrez_email'])
         model, errors = cobra.io.sbml.validate_sbml_model(config['polish_path'])
         print(errors)