Add print statements to track progress

wc_model_gen/eukaryote/complexation.py

@@ -56,7 +56,10 @@ def gen_reactions(self):
         amino_acid_id_conversion = self.options['amino_acid_id_conversion']
         codon_table = self.options['codon_table']
         cds = self.options['cds']
-
+
+        print('Start generating complexation submodel...')
+        assembly_rxn_no = 0
+        disassembly_rxn_no = 0
         for compl in cell.species_types.get(__type=wc_kb.core.ComplexSpeciesType):
 
             model_compl_species_type = model.species_types.get_one(id=compl.id)            
@@ -86,6 +89,8 @@ def gen_reactions(self):
                     model_rxn.participants.add(
                         model_compl_species.species_coefficients.get_or_create(coefficient=1))
 
+                    assembly_rxn_no += 1
+
                     # Generate reactions that lump complex dissociation and subunit degradation
                     for compl_subunit in compl.subunits:
 
@@ -103,6 +108,8 @@ def gen_reactions(self):
                                 model_compl_species.species_coefficients.get_or_create(
                                 coefficient=-1))
 
+                            disassembly_rxn_no += 1
+
                             for subunit in compl.subunits:
 
                                 model_subunit_species = model.species_types.get_one(
@@ -147,11 +154,13 @@ def gen_reactions(self):
                                     model_rxn.participants.add(
                                         model_subunit_species.species_coefficients.get_or_create(
                                         coefficient=subunit_coefficient))                              
-
+        print('{} reactions of complex assembly and {} reactions of complex dissociation have been generated'.format(
+            assembly_rxn_no, disassembly_rxn_no))
+
     def gen_rate_laws(self):
         """ Generate rate laws for the reactions in the submodel """
         model = self.model
-
+        rate_law_no = 0
         for reaction in self.submodel.reactions:
 
             if 'complex_association_' in reaction.id:
@@ -180,8 +189,10 @@ def gen_rate_laws(self):
                     expression=rate_law_exp,
                     reaction=reaction,
                     )
-            rate_law.id = rate_law.gen_id()    
-
+            rate_law.id = rate_law.gen_id() 
+            rate_law_no += 1
+
+        print('{} rate laws for complex assembly and dissociation have been generated'.format(rate_law_no))
 
     def calibrate_submodel(self):
         """ Calibrate the submodel using data in the KB """        
@@ -239,4 +250,6 @@ def calibrate_submodel(self):
                     species=degraded_subunit_species).coefficient                           
 
                 diss_k_cat = model.parameters.get_one(id='k_cat_{}'.format(reaction.id))
-                diss_k_cat.value = - degraded_subunit_stoic / degraded_subunit_hlife                    
+                diss_k_cat.value = - degraded_subunit_stoic / degraded_subunit_hlife
+
+        print('Complexation submodel has been generated')                                

wc_model_gen/eukaryote/initialize_model.py

@@ -27,6 +27,8 @@ def run(self):
         self.clean_and_validate_options()
         options = self.options
 
+        print('Model generator is being initialized')
+
         self.gen_taxon()
         self.gen_compartments()
         self.gen_parameters()
@@ -59,7 +61,9 @@ def run(self):
             self.gen_kb_rate_laws()
 
         if options['gen_environment']:
-            self.gen_environment()    
+            self.gen_environment()
+
+        print('Model generator has been initialized')        
 
     def clean_and_validate_options(self):
         options = self.options

wc_model_gen/eukaryote/rna_degradation.py

@@ -56,10 +56,12 @@ def gen_reactions(self):
                 'm': met_species_type.species.get_one(compartment=mitochondrion)
                 }
 
+        print('Start generating RNA degradation submodel...')
         # Create reaction for each RNA and get exosome
         rna_exo_pair = self.options.get('rna_exo_pair')
         rna_kbs = cell.species_types.get(__type=wc_kb.eukaryote_schema.TranscriptSpeciesType)
         self._degradation_modifier = {}
+        deg_rxn_no = 0
         for rna_kb in rna_kbs:  
 
             rna_kb_compartment_id = rna_kb.species[0].compartment.id
@@ -94,7 +96,10 @@ def gen_reactions(self):
 
             # Assign modifier
             self._degradation_modifier[reaction.name] = model.species_types.get_one(
-                name=rna_exo_pair[rna_kb.id]).species.get_one(compartment=degradation_compartment)        
+                name=rna_exo_pair[rna_kb.id]).species.get_one(compartment=degradation_compartment)
+
+            deg_rxn_no += 1
+        print('{} RNA degradation reactions have been generated'.format(deg_rxn_no))                
 
     def gen_rate_laws(self):
         """ Generate rate laws for the reactions in the submodel """
@@ -104,6 +109,7 @@ def gen_rate_laws(self):
         mitochondrion = model.compartments.get_one(id='m')
         cytoplasm = model.compartments.get_one(id='c')
 
+        rate_law_no = 0
         rnas_kb = cell.species_types.get(__type=wc_kb.eukaryote_schema.TranscriptSpeciesType)
         for rna_kb, reaction in zip(rnas_kb, self.submodel.reactions):
 
@@ -129,6 +135,9 @@ def gen_rate_laws(self):
                 reaction=reaction,
                 )
             rate_law.id = rate_law.gen_id()
+            rate_law_no += 1
+
+        print('{} rate laws for RNA degradation have been generated')    
 
     def calibrate_submodel(self):
         """ Calibrate the submodel using data in the KB """
@@ -187,4 +196,6 @@ def calibrate_submodel(self):
                 wc_lang.Compartment: {
                     rna_compartment.id: rna_compartment.init_volume.mean * rna_compartment.init_density.value,
                     degradation_compartment.id: degradation_compartment.init_volume.mean * degradation_compartment.init_density.value}
-            })       
+            })
+
+        print('RNA degradation submodel has been generated')           

wc_model_gen/eukaryote/transcription.py

@@ -113,7 +113,9 @@ def gen_reactions(self):
             volume='14',
             pages='796-806'
             )
-        ref_polr_distribution.id = 'ref_'+str(len(model.references))                    
+        ref_polr_distribution.id = 'ref_'+str(len(model.references))  
+
+        print('Start generating transcription submodel...')                  
 
         # Create for each RNA polymerase a reaction of binding to non-specific site        
         nuclear_genome_length = 0
@@ -204,6 +206,7 @@ def gen_reactions(self):
                 coefficient=1))
 
         # Create initiation and elongation reactions for each RNA
+        init_el_rxn_no = 0
         rna_kbs = cell.species_types.get(__type=wc_kb.eukaryote_schema.TranscriptSpeciesType)
         self._initiation_polr_species = {}
         self._elongation_modifier = {}
@@ -361,6 +364,11 @@ def gen_reactions(self):
                 polr_binding_site_species.species_coefficients.get_or_create(
                 coefficient=1))
 
+            init_el_rxn_no += 1
+
+        print('{} reactions each for initiation and elongation have been generated'.format(
+            init_el_rxn_no))    
+
     def gen_rate_laws(self):
         """ Generate rate laws for the reactions in the submodel """
 
@@ -471,7 +479,8 @@ def gen_rate_laws(self):
                 units=unit_registry.parse_units('s^-1')
                 )                    
 
-        # Generate rate laws for initiation and elongation & termination                    
+        # Generate rate laws for initiation and elongation & termination
+        rate_law_no = 0                    
         rnas_kb = cell.species_types.get(__type=wc_kb.eukaryote_schema.TranscriptSpeciesType)
         for rna_kb in rnas_kb:
 
@@ -596,7 +605,11 @@ def gen_rate_laws(self):
                 expression=rate_law_exp,
                 reaction=elongation_reaction,
                 )
-            rate_law.id = rate_law.gen_id()          
+            rate_law.id = rate_law.gen_id()
+
+            rate_law_no += 1
+
+        print('{} rate laws for initiation and elongation have been generated'.format(rate_law_no))              
 
     def calibrate_submodel(self):
         """ Calibrate the submodel using data in the KB """
@@ -747,3 +760,5 @@ def calibrate_submodel(self):
                     wc_lang.Compartment: {
                         rna_compartment.id: rna_compartment.init_volume.mean * rna_compartment.init_density.value},
                 })
+
+        print('Transcription submodel has been generated')