updated README.md with Python sample

README.md

@@ -38,63 +38,33 @@ Peter Schubert, Computational Cell Biology, HHU Duesseldorf, November 2021
 $ pip3 install  networkred@git+https://gitlab.cs.uni-duesseldorf.de/schubert/networkred.git
 ```
 
-## Small Python exampls
+## Small Python example
 
 ```python
 >>> import networkred
-
-import os
-import pandas as pd
-
-    data_dir = 'sample_data/data'
-    model_name = 'Deniz_model_fba'
-    protected_parts_file = 'Deniz_model_fba_nrp.xlsx'
-
-import networkred
-
-    original_sbml = 'sample_data/SBML_models/Deniz_model_fba.xml'
-    reduced_sbml = 'sample_data/SBML_models/Deniz_model_fba_red.xml'
-    
-    # import original SBML file
-    red_model = networkred.ReduceModel(original_sbml)
-
-    # set protected parts
-    
+>>> 
+>>> # file names
+>>> original_sbml = 'sample_data/SBML_models/Deniz_model_fba.xml'
+>>> reduced_sbml = 'sample_data/SBML_models/Deniz_model_fba_reduced.xml'
+>>> protected_parts = 'sample_data/data/Deniz_model_fba_nrp.xlsx'
     
-    protect_name = os.path.join(data_dir, protected_parts_file)
-    print('load reduction parameters from:', protect_name)
-    protect_rids = None
-    protect_mids = None
-    protect_funcs = None
-    with pd.ExcelFile(protect_name) as xlsx:
-        if 'reactions' in xlsx.sheet_names:
-            protect_rids = pd.read_excel(xlsx, sheet_name='reactions', index_col=0).index.tolist()
-        if 'metabolites' in xlsx.sheet_names:
-            protect_mids = pd.read_excel(xlsx, sheet_name='metabolites', index_col=0).index.tolist()
-        if 'functions' in xlsx.sheet_names:
-            protect_funcs = pd.read_excel(xlsx, sheet_name='functions', index_col=0)
-        if 'bounds' in xlsx.sheet_names:
-            temp_fbc_bounds = pd.read_excel(xlsx, sheet_name='bounds', index_col=0)
-    red_model.set_reduction_params(protect_rids=protect_rids,
-                                   protect_mids=protect_mids,
-                                   protect_funcs=protect_funcs,
-                                   temp_fbc_bounds=temp_fbc_bounds,
-                                   model_base='original')
-
-    # reduce the network
-    red_model.reduce()
-
-    # export reduced model to sbml
-    red_model.write_sbml(reduced_sbml)
-
-
+>>> # load the original model
+>>> red_model = networkred.ReduceModel(original_sbml)
+
+>>> # load and configure protected parts for network reduction
+>>> nrp = networkred.load_raw_protected_data(protected_parts)
+>>> red_model.set_reduction_params(protect_rids=nrp['reactions'],
+                                   protect_mids=nrp['metabolites'],
+                                   protect_funcs=nrp['functions'],
+                                   temp_fbc_bounds=nrp['bounds'])
+>>>  # reduce the network
+>>> red_model.reduce()
 >>> 
+>>> # export reduced model to sbml
+>>> red_model.write_sbml(reduced_sbml)
 ```
 
 
-
-
-
 ## License
 
 [GPLv3](LICENSE.txt)

networkred/reduce_model.py

@@ -433,7 +433,7 @@ class ReduceModel:
                 blocked_rids = find_blocked_reactions(self._red_model, reaction_list=rs, processes=self._cpus)
                 if len(blocked_rids) > 0:
                     print('protected reactions that are blocked:', ', '.join(blocked_rids))
-                    logging.warning('protected reactions that are blocked: %s', ', '.join(blocked_rids))
+                    logging.info('protected reactions that are blocked: %s', ', '.join(blocked_rids))
                     return False
                 else:
                     logging.info('protected reactions are feasible')
@@ -456,7 +456,7 @@ class ReduceModel:
                             blocked_mids.add(mid)
                     if len(blocked_mids) > 0:
                         print('protected metabolites that are blocked:', ', '.join(blocked_mids))
-                        logging.warning('protected metabolites that are blocked: %s', ', '.join(blocked_mids))
+                        logging.info('protected metabolites that are blocked: %s', ', '.join(blocked_mids))
                         return False
                     else:
                         logging.info('protected metabolites are feasible')
@@ -469,14 +469,14 @@ class ReduceModel:
                 self._add_constraints(k)
                 if np.isnan(self._red_model.slim_optimize()):
                     print('FVA for protected function %d failed', k)
-                    logging.warning('FVA for protected function %d failed', k)
+                    logging.info('FVA for protected function %d failed', k)
                     self._remove_constraints()
                     return False
                 self._remove_constraints()
         else:
             if np.isnan(self._red_model.slim_optimize()):
                 print('FVA failed')
-                logging.warning('FVA failed')
+                logging.info('FVA failed')
                 return False
 
         logging.info('feasibility checked and OK')

sample_reduce_model.py

@@ -27,7 +27,7 @@ def reduce_model():
     print('networkred version: {:s}'.format(networkred.__version__))
     print('working directory :', os.getcwd())
 
-    # file names and directories
+    # file names
     original_sbml = 'sample_data/SBML_models/Deniz_model_fba.xml'
     reduced_sbml = 'sample_data/SBML_models/Deniz_model_fba_reduced.xml'
     protected_parts = 'sample_data/data/Deniz_model_fba_nrp.xlsx'
@@ -35,7 +35,7 @@ def reduce_model():
     # load the original model
     red_model = networkred.ReduceModel(original_sbml)
 
-    # load protected parts for network reduction
+    # load and configure protected parts for network reduction
     nrp = networkred.load_raw_protected_data(protected_parts)
     red_model.set_reduction_params(protect_rids=nrp['reactions'],
                                    protect_mids=nrp['metabolites'],