gsrap 0.7.0__py3-none-any.whl → 0.7.1__py3-none-any.whl

gsrap/.ipynb_checkpoints/__init__-checkpoint.py

@@ -1,8 +1,10 @@
 import argparse
 import sys
 import traceback
+import requests
 import importlib.metadata
 from datetime import datetime
+from packaging import version
 
 
 import cobra
@@ -29,8 +31,9 @@ solver_name = solver_name.replace("_interface", '')
 def main():
     
     
-    # define the header of main- and sub-commands. 
-    header = f'gsrap v{importlib.metadata.metadata("gsrap")["Version"]},\ndeveloped by Gioele Lazzari (gioele.lazzari@univr.it).'
+    # define the header of main- and sub-commands.
+    current_version = importlib.metadata.metadata("gsrap")["Version"]
+    header = f'gsrap v{current_version},\ndeveloped by Gioele Lazzari (gioele.lazzari@univr.it).'
     
     
     # create the command line arguments:
@@ -117,12 +120,36 @@ def main():
     # set up the logger:
     logger = get_logger('gsrap', args.verbose)
     
-    
+        
     
     # show a welcome message:
     set_header_trailer_formatter(logger.handlers[0])
     logger.info(header + '\n')
-    command_line = '' # print the full command line:
+    
+    
+    
+    # check if newer version is available
+    try:
+        response = requests.get(f"https://pypi.org/pypi/gsrap/json", timeout=3)  # sends an HTTP GET request to the given URL
+        response.raise_for_status()  # check the HTTP status code (e.g. 200, 404, 500): if not in the 2xx success range, raise requests.exceptions.HTTPError
+        data = response.json()
+        newest_version = data["info"]["version"] 
+    except Exception as error:  # eg requests.exceptions.Timeout, requests.exceptions.HTTPError
+        logger.info(f'Can\'t retrieve the number of the newest version. Please contact the developer reporting the following error: "{error}".')
+        logger.info('')  # still no formatting here
+        # do not exit, continue with the program
+    if version.parse(current_version) < version.parse(newest_version):
+        warning_message = f"███ Last version is v{newest_version} and you have v{current_version}: please update gsrap! ███"
+        border = ''.join(['█' for i in range(len(warning_message))])
+        logger.info(border)
+        logger.info(warning_message)
+        logger.info(border)
+        logger.info('')  # still no formatting here
+    
+    
+    
+    # print the full command line:
+    command_line = '' 
     for arg, value in vars(args).items():
         if arg == 'subcommand': command_line = command_line + f"gsrap {value} "
         else: command_line = command_line + f"--{arg} {value} "

gsrap/__init__.py

@@ -1,8 +1,10 @@
 import argparse
 import sys
 import traceback
+import requests
 import importlib.metadata
 from datetime import datetime
+from packaging import version
 
 
 import cobra
@@ -29,8 +31,9 @@ solver_name = solver_name.replace("_interface", '')
 def main():
     
     
-    # define the header of main- and sub-commands. 
-    header = f'gsrap v{importlib.metadata.metadata("gsrap")["Version"]},\ndeveloped by Gioele Lazzari (gioele.lazzari@univr.it).'
+    # define the header of main- and sub-commands.
+    current_version = importlib.metadata.metadata("gsrap")["Version"]
+    header = f'gsrap v{current_version},\ndeveloped by Gioele Lazzari (gioele.lazzari@univr.it).'
     
     
     # create the command line arguments:
@@ -117,12 +120,36 @@ def main():
     # set up the logger:
     logger = get_logger('gsrap', args.verbose)
     
-    
+        
     
     # show a welcome message:
     set_header_trailer_formatter(logger.handlers[0])
     logger.info(header + '\n')
-    command_line = '' # print the full command line:
+    
+    
+    
+    # check if newer version is available
+    try:
+        response = requests.get(f"https://pypi.org/pypi/gsrap/json", timeout=3)  # sends an HTTP GET request to the given URL
+        response.raise_for_status()  # check the HTTP status code (e.g. 200, 404, 500): if not in the 2xx success range, raise requests.exceptions.HTTPError
+        data = response.json()
+        newest_version = data["info"]["version"] 
+    except Exception as error:  # eg requests.exceptions.Timeout, requests.exceptions.HTTPError
+        logger.info(f'Can\'t retrieve the number of the newest version. Please contact the developer reporting the following error: "{error}".')
+        logger.info('')  # still no formatting here
+        # do not exit, continue with the program
+    if version.parse(current_version) < version.parse(newest_version):
+        warning_message = f"███ Last version is v{newest_version} and you have v{current_version}: please update gsrap! ███"
+        border = ''.join(['█' for i in range(len(warning_message))])
+        logger.info(border)
+        logger.info(warning_message)
+        logger.info(border)
+        logger.info('')  # still no formatting here
+    
+    
+    
+    # print the full command line:
+    command_line = '' 
     for arg, value in vars(args).items():
         if arg == 'subcommand': command_line = command_line + f"gsrap {value} "
         else: command_line = command_line + f"--{arg} {value} "

gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py

@@ -190,6 +190,10 @@ def introduce_universal_biomass(logger, dbexp, universe):
     r.build_reaction_from_string(rstring)
     
     
+    # add SBO annotation
+    r.annotation['sbo'] = ['SBO:0000629']  # biomass reaction 
+    
+    
     # set as objective:
     universe.objective = 'Biomass'
     

gsrap/commons/.ipynb_checkpoints/coeffs-checkpoint.py

@@ -267,7 +267,7 @@ def compute_exp_LIPIDS_coeffs(logger, model, MWF, LIPIDS_PL, LIPIDS_FA):
     r.bounds = (0, 1000)
     r.gene_reaction_rule = 'spontaneous'   
     r.update_genes_from_gpr()
-    
+
     
     # determine 'L' formula and charge (charge should be -1 like every fatty acid)
     L_dict = dict()              # for 1 mol

gsrap/commons/.ipynb_checkpoints/fluxbal-checkpoint.py

@@ -44,7 +44,7 @@ def verify_growth(model, boolean=True):
         if status =='infeasible':
             return 'infeasible'
         elif obj_value < get_optthr():
-            return 0
+            return 0.0
         else:
             return round(obj_value, 3)
         

gsrap/commons/biomass.py

@@ -190,6 +190,10 @@ def introduce_universal_biomass(logger, dbexp, universe):
     r.build_reaction_from_string(rstring)
     
     
+    # add SBO annotation
+    r.annotation['sbo'] = ['SBO:0000629']  # biomass reaction 
+    
+    
     # set as objective:
     universe.objective = 'Biomass'
     

gsrap/commons/coeffs.py

@@ -267,7 +267,7 @@ def compute_exp_LIPIDS_coeffs(logger, model, MWF, LIPIDS_PL, LIPIDS_FA):
     r.bounds = (0, 1000)
     r.gene_reaction_rule = 'spontaneous'   
     r.update_genes_from_gpr()
-    
+
     
     # determine 'L' formula and charge (charge should be -1 like every fatty acid)
     L_dict = dict()              # for 1 mol

gsrap/commons/fluxbal.py

@@ -44,7 +44,7 @@ def verify_growth(model, boolean=True):
         if status =='infeasible':
             return 'infeasible'
         elif obj_value < get_optthr():
-            return 0
+            return 0.0
         else:
             return round(obj_value, 3)
         

gsrap/mkmodel/.ipynb_checkpoints/gapfillutils-checkpoint.py

@@ -33,6 +33,9 @@ def import_from_universe(model, universe, rid, bounds=None, gpr=None):
     else:
         r.gene_reaction_rule = ''
     r.update_genes_from_gpr()
+    
+    # set annotations
+    r.annotation = ru.annotation
 
 
 

gsrap/mkmodel/.ipynb_checkpoints/mkmodel-checkpoint.py

@@ -64,6 +64,7 @@ def create_model_incore(params):
     # remove universal orphans
     model = remove_universal_orphans(logger, model)
 
+    
 
     ###### PRUNING
     logger.info("Reading provided eggnog-mapper annotation...")
@@ -77,6 +78,7 @@ def create_model_incore(params):
     translate_remaining_kos(logger, model, eggnog_ko_to_gids)
     restore_gene_annotations(logger, model, universe, eggonog_gid_to_kos)
 
+    
 
     ###### GAPFILLING
     # force inclusion of reactions:  
@@ -103,30 +105,35 @@ def create_model_incore(params):
     if type(df_P)==int: return 1
 
 
-    ###### POLISHING 2
-    # remove disconnected metabolites
-    model = remove_disconnected(logger, model)
 
+    ###### POLISHING 2
     # remove unsed sinks and demands
     model = remove_sinks_demands(logger, model)  
+    
+    # remove disconnected metabolites
+    model = remove_disconnected(logger, model)
 
+    
 
     # # # # #   DERIVATION ENDS HERE   # # # # #
     log_metrics(logger, model)
     log_unbalances(logger, model)
 
 
+    
     ###### CHECKS
     # check blocked metabolites / dead-ends
     df_S = biosynthesis_on_media(logger, model, dbexp, args.gap_fill, args.biosynth)
     if type(df_S)==int: return 1
 
 
+
     ###### POLISHING 3
     # reset growth environment befor saving the model
     gempipe.reset_growth_env(model)
 
 
+    
     # output the model:
     logger.info("Writing strain-specific model...")
     cobra.io.save_json_model(model, f'{args.outdir}/{model.id}.json')        # JSON

gsrap/mkmodel/gapfillutils.py

@@ -33,6 +33,9 @@ def import_from_universe(model, universe, rid, bounds=None, gpr=None):
     else:
         r.gene_reaction_rule = ''
     r.update_genes_from_gpr()
+    
+    # set annotations
+    r.annotation = ru.annotation
 
 
 

gsrap/mkmodel/mkmodel.py

@@ -64,6 +64,7 @@ def create_model_incore(params):
     # remove universal orphans
     model = remove_universal_orphans(logger, model)
 
+    
 
     ###### PRUNING
     logger.info("Reading provided eggnog-mapper annotation...")
@@ -77,6 +78,7 @@ def create_model_incore(params):
     translate_remaining_kos(logger, model, eggnog_ko_to_gids)
     restore_gene_annotations(logger, model, universe, eggonog_gid_to_kos)
 
+    
 
     ###### GAPFILLING
     # force inclusion of reactions:  
@@ -103,30 +105,35 @@ def create_model_incore(params):
     if type(df_P)==int: return 1
 
 
-    ###### POLISHING 2
-    # remove disconnected metabolites
-    model = remove_disconnected(logger, model)
 
+    ###### POLISHING 2
     # remove unsed sinks and demands
     model = remove_sinks_demands(logger, model)  
+    
+    # remove disconnected metabolites
+    model = remove_disconnected(logger, model)
 
+    
 
     # # # # #   DERIVATION ENDS HERE   # # # # #
     log_metrics(logger, model)
     log_unbalances(logger, model)
 
 
+    
     ###### CHECKS
     # check blocked metabolites / dead-ends
     df_S = biosynthesis_on_media(logger, model, dbexp, args.gap_fill, args.biosynth)
     if type(df_S)==int: return 1
 
 
+
     ###### POLISHING 3
     # reset growth environment befor saving the model
     gempipe.reset_growth_env(model)
 
 
+    
     # output the model:
     logger.info("Writing strain-specific model...")
     cobra.io.save_json_model(model, f'{args.outdir}/{model.id}.json')        # JSON

gsrap/parsedb/.ipynb_checkpoints/annotation-checkpoint.py

@@ -66,6 +66,9 @@ def translate_annotate_genes(logger, model, idcollection_dict):
             g.annotation['ec'] = list(ko_to_ecs[ko])
             g.annotation['cog'] = list(ko_to_cogs[ko])
             g.annotation['go'] = list(ko_to_gos[ko])
+            
+        # add SBO annotation
+        g.annotation['sbo'] = ['SBO:0000243']  # demand reaction 
         
     
         

gsrap/parsedb/.ipynb_checkpoints/completeness-checkpoint.py

@@ -43,10 +43,10 @@ def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, i
         for eggfile in eggnog:
             eggset = parse_eggnog(model, eggfile, idcollection_dict)
             kr_uni = kr_uni.union(eggset)
-        kr_uni_label = f"'{len(eggnog)} eggnog annotations'"
+        kr_uni_label = f"{len(eggnog)} eggnog annotations"
     else: 
         kr_uni = idcollection_dict['kr']
-        kr_uni_label = "'whole KEGG'"
+        kr_uni_label = "whole KEGG"
     
     
     # get all the 'kr' annotations in the model
@@ -55,7 +55,10 @@ def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, i
         if 'kegg.reaction' in r.annotation.keys():
             for kr_id in r.annotation['kegg.reaction']:
                 kr_ids_modeled.add(kr_id)
-    logger.info(f"Universe coverage for {kr_uni_label}: {round(len(kr_ids_modeled.intersection(kr_uni))/len(kr_uni)*100, 0)}%!")
+    kr_uni_missing = len(kr_uni - kr_ids_modeled.intersection(kr_uni))
+    kr_uni_coverage = len(kr_ids_modeled.intersection(kr_uni)) / len(kr_uni) * 100
+    logger.info(f"Coverage for '{kr_uni_label}': {round(kr_uni_coverage, 0)}% ({kr_uni_missing} missing).")
+    
     
     
     # get all the map / md codes:
@@ -147,7 +150,7 @@ def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, i
                 'missing': missing,
                 'md_ids': [j['md_id'] for j in i['mds']],
             })
-                
+            
             
     # order list by '%' of completness and print:
     list_coverage = sorted(list_coverage, key=lambda x: x['perc_completeness'], reverse=True)

gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py

@@ -141,6 +141,10 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
         # save as list: 
         for ankey in ankeys:
             m.annotation[ankey] = list(m.annotation[ankey])
+            
+            
+        # add SBO annotation
+        m.annotation['sbo'] = ['SBO:0000247']  # generic metabolite
    
         
     
@@ -264,7 +268,8 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
         m_e.name = m_c.name
         m_e.formula = m_c.formula
         m_e.charge = m_c.charge
-        m_e.annotation = m_c.annotation
+        
+        m_e.annotation = m_c.annotation   # transfer all annotations, including SBO!
             
     
     def add_exchange_reaction(model, mid_e):
@@ -283,6 +288,10 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
             r.bounds = (-1000, 1000)
         else:
             r.bounds = (0, 1000)
+            
+        # add SBO annotation
+        r.annotation['sbo'] = ['SBO:0000627']  # exchange reaction    
+        
     
     
     
@@ -418,6 +427,9 @@ def introduce_sinks_demands(logger, model):
         r.name = f"Sink for {model.metabolites.get_by_id(f'{puremid}_c').name}"
         r.build_reaction_from_string(f'{puremid}_c <=> ')
         r.bounds = (-1000, 1000)
+        
+        # add SBO annotation
+        r.annotation['sbo'] = ['SBO:0000632']  # sink reaction 
     
     
     for puremid in demands: 
@@ -427,6 +439,9 @@ def introduce_sinks_demands(logger, model):
         r.name = f"Demand for {model.metabolites.get_by_id(f'{puremid}_c').name}"
         r.build_reaction_from_string(f'{puremid}_c --> ')
         r.bounds = (0, 1000)
+        
+        # add SBO annotation
+        r.annotation['sbo'] = ['SBO:0000628']  # demand reaction 
     
     
     return model

gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py

@@ -113,7 +113,7 @@ def main(args, logger):
     
     ###### RECONSTRUCTION
     # create the model
-    universe = cobra.Model('newuni')   
+    universe = cobra.Model('universe')   
     logger.info("Parsing gsrap database...")
     
     # introduce M / R / T

gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py

@@ -125,6 +125,13 @@ def add_reaction(logger, model, rid, row, kr_ids, kegg_reaction_to_others, addty
         r.annotation[ankey] = list(r.annotation[ankey])
         
         
+    # add SBO annotation
+    if addtype=='R':
+        r.annotation['sbo'] = ['SBO:0000176']  # metabolic reaction
+    else:
+        r.annotation['sbo'] = ['SBO:0000185']  # transport reaction
+        
+        
     # check if unbalanced
     if r.check_mass_balance() != {}: 
         logger.error(f"{itemtype} '{r.id}' is unbalanced: {r.check_mass_balance()}.")

gsrap/parsedb/annotation.py

@@ -66,6 +66,9 @@ def translate_annotate_genes(logger, model, idcollection_dict):
             g.annotation['ec'] = list(ko_to_ecs[ko])
             g.annotation['cog'] = list(ko_to_cogs[ko])
             g.annotation['go'] = list(ko_to_gos[ko])
+            
+        # add SBO annotation
+        g.annotation['sbo'] = ['SBO:0000243']  # demand reaction 
         
     
         

gsrap/parsedb/completeness.py

@@ -43,10 +43,10 @@ def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, i
         for eggfile in eggnog:
             eggset = parse_eggnog(model, eggfile, idcollection_dict)
             kr_uni = kr_uni.union(eggset)
-        kr_uni_label = f"'{len(eggnog)} eggnog annotations'"
+        kr_uni_label = f"{len(eggnog)} eggnog annotations"
     else: 
         kr_uni = idcollection_dict['kr']
-        kr_uni_label = "'whole KEGG'"
+        kr_uni_label = "whole KEGG"
     
     
     # get all the 'kr' annotations in the model
@@ -55,7 +55,10 @@ def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, i
         if 'kegg.reaction' in r.annotation.keys():
             for kr_id in r.annotation['kegg.reaction']:
                 kr_ids_modeled.add(kr_id)
-    logger.info(f"Universe coverage for {kr_uni_label}: {round(len(kr_ids_modeled.intersection(kr_uni))/len(kr_uni)*100, 0)}%!")
+    kr_uni_missing = len(kr_uni - kr_ids_modeled.intersection(kr_uni))
+    kr_uni_coverage = len(kr_ids_modeled.intersection(kr_uni)) / len(kr_uni) * 100
+    logger.info(f"Coverage for '{kr_uni_label}': {round(kr_uni_coverage, 0)}% ({kr_uni_missing} missing).")
+    
     
     
     # get all the map / md codes:
@@ -147,7 +150,7 @@ def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, i
                 'missing': missing,
                 'md_ids': [j['md_id'] for j in i['mds']],
             })
-                
+            
             
     # order list by '%' of completness and print:
     list_coverage = sorted(list_coverage, key=lambda x: x['perc_completeness'], reverse=True)

gsrap/parsedb/introduce.py

@@ -141,6 +141,10 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
         # save as list: 
         for ankey in ankeys:
             m.annotation[ankey] = list(m.annotation[ankey])
+            
+            
+        # add SBO annotation
+        m.annotation['sbo'] = ['SBO:0000247']  # generic metabolite
    
         
     
@@ -264,7 +268,8 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
         m_e.name = m_c.name
         m_e.formula = m_c.formula
         m_e.charge = m_c.charge
-        m_e.annotation = m_c.annotation
+        
+        m_e.annotation = m_c.annotation   # transfer all annotations, including SBO!
             
     
     def add_exchange_reaction(model, mid_e):
@@ -283,6 +288,10 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
             r.bounds = (-1000, 1000)
         else:
             r.bounds = (0, 1000)
+            
+        # add SBO annotation
+        r.annotation['sbo'] = ['SBO:0000627']  # exchange reaction    
+        
     
     
     
@@ -418,6 +427,9 @@ def introduce_sinks_demands(logger, model):
         r.name = f"Sink for {model.metabolites.get_by_id(f'{puremid}_c').name}"
         r.build_reaction_from_string(f'{puremid}_c <=> ')
         r.bounds = (-1000, 1000)
+        
+        # add SBO annotation
+        r.annotation['sbo'] = ['SBO:0000632']  # sink reaction 
     
     
     for puremid in demands: 
@@ -427,6 +439,9 @@ def introduce_sinks_demands(logger, model):
         r.name = f"Demand for {model.metabolites.get_by_id(f'{puremid}_c').name}"
         r.build_reaction_from_string(f'{puremid}_c --> ')
         r.bounds = (0, 1000)
+        
+        # add SBO annotation
+        r.annotation['sbo'] = ['SBO:0000628']  # demand reaction 
     
     
     return model

gsrap/parsedb/parsedb.py

@@ -113,7 +113,7 @@ def main(args, logger):
     
     ###### RECONSTRUCTION
     # create the model
-    universe = cobra.Model('newuni')   
+    universe = cobra.Model('universe')   
     logger.info("Parsing gsrap database...")
     
     # introduce M / R / T

gsrap/parsedb/repeating.py

@@ -125,6 +125,13 @@ def add_reaction(logger, model, rid, row, kr_ids, kegg_reaction_to_others, addty
         r.annotation[ankey] = list(r.annotation[ankey])
         
         
+    # add SBO annotation
+    if addtype=='R':
+        r.annotation['sbo'] = ['SBO:0000176']  # metabolic reaction
+    else:
+        r.annotation['sbo'] = ['SBO:0000185']  # transport reaction
+        
+        
     # check if unbalanced
     if r.check_mass_balance() != {}: 
         logger.error(f"{itemtype} '{r.id}' is unbalanced: {r.check_mass_balance()}.")

gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py

@@ -12,9 +12,7 @@ from ..commons import verify_growth
 def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
     
     
-    # if working with the universe:
-    if universe_in_parsedb:
-        log_for_parsedb = []
+
     
     
     # check if requested
@@ -58,7 +56,10 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
         res_fba = verify_growth(model, boolean=False)
         df_G.loc[obj_id, f'{medium}'] = res_fba
         if universe_in_parsedb:
-            log_for_parsedb.append(f"'{medium}': {res_fba}")
+            if res_fba == 'infeasible' or res_fba == 0.0:
+                logger.warning(f"Growth on '{medium}': {res_fba}.")
+            else:
+                logger.info(f"Growth on '{medium}': {res_fba}.")
         
         
         # perform FVA if requested:
@@ -68,7 +69,5 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
             for rid, row in df_fva.iterrows():
                 df_G.loc[rid, f'{medium}'] = f"({round(row['minimum'], 3)}, {round(row['maximum'], 3)})"
 
-    
-    if universe_in_parsedb:
-        logger.info(f"Results: {'; '.join(log_for_parsedb)}.")
+
     return df_G

gsrap/runsims/simplegrowth.py

@@ -12,9 +12,7 @@ from ..commons import verify_growth
 def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
     
     
-    # if working with the universe:
-    if universe_in_parsedb:
-        log_for_parsedb = []
+
     
     
     # check if requested
@@ -58,7 +56,10 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
         res_fba = verify_growth(model, boolean=False)
         df_G.loc[obj_id, f'{medium}'] = res_fba
         if universe_in_parsedb:
-            log_for_parsedb.append(f"'{medium}': {res_fba}")
+            if res_fba == 'infeasible' or res_fba == 0.0:
+                logger.warning(f"Growth on '{medium}': {res_fba}.")
+            else:
+                logger.info(f"Growth on '{medium}': {res_fba}.")
         
         
         # perform FVA if requested:
@@ -68,7 +69,5 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
             for rid, row in df_fva.iterrows():
                 df_G.loc[rid, f'{medium}'] = f"({round(row['minimum'], 3)}, {round(row['maximum'], 3)})"
 
-    
-    if universe_in_parsedb:
-        logger.info(f"Results: {'; '.join(log_for_parsedb)}.")
+
     return df_G

{gsrap-0.7.0.dist-info → gsrap-0.7.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: gsrap
-Version: 0.7.0
+Version: 0.7.1
 Summary: 
 License: GNU General Public License v3.0
 Author: Gioele Lazzari

{gsrap-0.7.0.dist-info → gsrap-0.7.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
-gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=OKMs5wy3RsxLLsD-fOfF0MCVKaxUOtlemcGa3ywyKWI,12390
-gsrap/__init__.py,sha256=OKMs5wy3RsxLLsD-fOfF0MCVKaxUOtlemcGa3ywyKWI,12390
+gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=93coHbPQfWL7XSudRvKh5RGgqJbyOvECVmMaHPfShOU,13693
+gsrap/__init__.py,sha256=93coHbPQfWL7XSudRvKh5RGgqJbyOvECVmMaHPfShOU,13693
 gsrap/assets/.ipynb_checkpoints/PM1-checkpoint.csv,sha256=0qjaMVG_t9aFxbHbxON6ecmEUnWPwN9nhmxc61QFeCU,8761
 gsrap/assets/.ipynb_checkpoints/PM2A-checkpoint.csv,sha256=rjYTdwe8lpRS552BYiUP3J71juG2ywVdR5Sux6fjZTY,8816
 gsrap/assets/.ipynb_checkpoints/PM3B-checkpoint.csv,sha256=42IGX_2O5bRYSiHoMuVKT-T-bzVj0cSRZBvGOrbnQMA,8130
@@ -12,23 +12,23 @@ gsrap/assets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gsrap/assets/kegg_compound_to_others.pickle,sha256=pz1897cfQ7PLsYZiBVcoMQPzvRzT-nHUdgphBe0g5ZQ,8233860
 gsrap/assets/kegg_reaction_to_others.pickle,sha256=AGW8CGN5hKeXZoYn3JRF4Xu832WyNrTlMcLw7luttlc,1703146
 gsrap/commons/.ipynb_checkpoints/__init__-checkpoint.py,sha256=P_rdjFcL_FjkKYT3a0IJiQTzWL7p2Hm6z-hjuCZEHgU,216
-gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py,sha256=P5jjB-oIgHyYEqPIKsC_Ik1xhiiJzi_piVd-zPaBzg4,17889
-gsrap/commons/.ipynb_checkpoints/coeffs-checkpoint.py,sha256=wDh7VhTQrFpRKe2ijbnBU6cXjoeEvJxed6eNEBx-8Yc,19186
+gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py,sha256=4u7WBaUgo42tBoXDU1D0VUjICatb44e0jfswZrBeHYs,17987
+gsrap/commons/.ipynb_checkpoints/coeffs-checkpoint.py,sha256=qI3_GuqHkeA2KbK9pYdkqJaFwYemAVZJGLRR4QtHt6w,19182
 gsrap/commons/.ipynb_checkpoints/downloads-checkpoint.py,sha256=JFrOYXrzLFhclwMtLmq8xo0QZVyjEn7QfzaTRad7y6I,8460
 gsrap/commons/.ipynb_checkpoints/escherutils-checkpoint.py,sha256=lftRIKAbP4eztaZM83V3LKWZK4DtKDuCiC9A46paVoM,1148
 gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py,sha256=XO7ZZFqORB1nnH1Nj07VSGr18em1rt_AH6oAqwqhp4o,5867
-gsrap/commons/.ipynb_checkpoints/fluxbal-checkpoint.py,sha256=ZXbC6DjW5mAPaF5POh98mQHDWl9a7t9q6GFx9IlVs9g,1260
+gsrap/commons/.ipynb_checkpoints/fluxbal-checkpoint.py,sha256=jgC3-vI9Tbjvqohh2mJwFra4rl_pbUzHWrSa_QAxVO4,1262
 gsrap/commons/.ipynb_checkpoints/logutils-checkpoint.py,sha256=VsnrkIsUftS3MOOwAd0n0peQ7a2X5ZEx930eCtzmW7g,1317
 gsrap/commons/.ipynb_checkpoints/medium-checkpoint.py,sha256=VYKN8X1PNERP6uQDbznZXfgflLEvnw4j1T8AIAdrE7s,2902
 gsrap/commons/.ipynb_checkpoints/metrics-checkpoint.py,sha256=gvqF2c0e31m5qQWQ11JF4-eMqxtuONy_7lUiC7uaXX4,3291
 gsrap/commons/.ipynb_checkpoints/sbmlutils-checkpoint.py,sha256=gkY02qbGXrbYStn2F8J0KM0fmqati2Nbvi128EF7coI,365
 gsrap/commons/__init__.py,sha256=P_rdjFcL_FjkKYT3a0IJiQTzWL7p2Hm6z-hjuCZEHgU,216
-gsrap/commons/biomass.py,sha256=P5jjB-oIgHyYEqPIKsC_Ik1xhiiJzi_piVd-zPaBzg4,17889
-gsrap/commons/coeffs.py,sha256=wDh7VhTQrFpRKe2ijbnBU6cXjoeEvJxed6eNEBx-8Yc,19186
+gsrap/commons/biomass.py,sha256=4u7WBaUgo42tBoXDU1D0VUjICatb44e0jfswZrBeHYs,17987
+gsrap/commons/coeffs.py,sha256=qI3_GuqHkeA2KbK9pYdkqJaFwYemAVZJGLRR4QtHt6w,19182
 gsrap/commons/downloads.py,sha256=JFrOYXrzLFhclwMtLmq8xo0QZVyjEn7QfzaTRad7y6I,8460
 gsrap/commons/escherutils.py,sha256=lftRIKAbP4eztaZM83V3LKWZK4DtKDuCiC9A46paVoM,1148
 gsrap/commons/excelhub.py,sha256=XO7ZZFqORB1nnH1Nj07VSGr18em1rt_AH6oAqwqhp4o,5867
-gsrap/commons/fluxbal.py,sha256=ZXbC6DjW5mAPaF5POh98mQHDWl9a7t9q6GFx9IlVs9g,1260
+gsrap/commons/fluxbal.py,sha256=jgC3-vI9Tbjvqohh2mJwFra4rl_pbUzHWrSa_QAxVO4,1262
 gsrap/commons/logutils.py,sha256=VsnrkIsUftS3MOOwAd0n0peQ7a2X5ZEx930eCtzmW7g,1317
 gsrap/commons/medium.py,sha256=VYKN8X1PNERP6uQDbznZXfgflLEvnw4j1T8AIAdrE7s,2902
 gsrap/commons/metrics.py,sha256=gvqF2c0e31m5qQWQ11JF4-eMqxtuONy_7lUiC7uaXX4,3291
@@ -42,31 +42,31 @@ gsrap/getmaps/kdown.py,sha256=mv5wqP4DX9KhB1IIWx6cLrc-MjQdF5Nz-Gii8QSO_6I,24498
 gsrap/mkmodel/.ipynb_checkpoints/__init__-checkpoint.py,sha256=PNze-26HMOwfdJ92KiXpr--VV1ftVfo3CAxBZgeokp8,92
 gsrap/mkmodel/.ipynb_checkpoints/biologcuration-checkpoint.py,sha256=Nn7z-js-mzzeO23kVM2L7sJ5PNle7AkCUeBcEAYjlFU,15378
 gsrap/mkmodel/.ipynb_checkpoints/gapfill-checkpoint.py,sha256=BPZw4sszlBhAYfHnV0pA7EpG0b2ePwS6kUfFt0Ww-ss,5159
-gsrap/mkmodel/.ipynb_checkpoints/gapfillutils-checkpoint.py,sha256=XEuiX_38HBDYWOM6wVSY6UI9nuqbo9pzLOhERSt1P-g,3063
-gsrap/mkmodel/.ipynb_checkpoints/mkmodel-checkpoint.py,sha256=cS8h5TTPjqzaw9jlIbb-MUfEFkHHEo59oEHItID_hvc,8506
+gsrap/mkmodel/.ipynb_checkpoints/gapfillutils-checkpoint.py,sha256=S6nFUZ1Bbdf13nVJhGK2S5C_V3hd5zwTg2o5nzejngg,3123
+gsrap/mkmodel/.ipynb_checkpoints/mkmodel-checkpoint.py,sha256=bXKBU8sUhRWKU-MYqiHgZFEwqvpAtoJa6_1h6D94REM,8537
 gsrap/mkmodel/.ipynb_checkpoints/polishing-checkpoint.py,sha256=R1UdFPxN8N27Iu0jsYW2N_1BkWEbBHaMYW6NkCYZK_k,3256
 gsrap/mkmodel/.ipynb_checkpoints/pruner-checkpoint.py,sha256=BVOK1iFXpTgZswDgAv-TgHxKB6W3iucIAo1XWrAbu4A,7009
 gsrap/mkmodel/__init__.py,sha256=PNze-26HMOwfdJ92KiXpr--VV1ftVfo3CAxBZgeokp8,92
 gsrap/mkmodel/biologcuration.py,sha256=Nn7z-js-mzzeO23kVM2L7sJ5PNle7AkCUeBcEAYjlFU,15378
 gsrap/mkmodel/gapfill.py,sha256=BPZw4sszlBhAYfHnV0pA7EpG0b2ePwS6kUfFt0Ww-ss,5159
-gsrap/mkmodel/gapfillutils.py,sha256=XEuiX_38HBDYWOM6wVSY6UI9nuqbo9pzLOhERSt1P-g,3063
-gsrap/mkmodel/mkmodel.py,sha256=cS8h5TTPjqzaw9jlIbb-MUfEFkHHEo59oEHItID_hvc,8506
+gsrap/mkmodel/gapfillutils.py,sha256=S6nFUZ1Bbdf13nVJhGK2S5C_V3hd5zwTg2o5nzejngg,3123
+gsrap/mkmodel/mkmodel.py,sha256=bXKBU8sUhRWKU-MYqiHgZFEwqvpAtoJa6_1h6D94REM,8537
 gsrap/mkmodel/polishing.py,sha256=R1UdFPxN8N27Iu0jsYW2N_1BkWEbBHaMYW6NkCYZK_k,3256
 gsrap/mkmodel/pruner.py,sha256=BVOK1iFXpTgZswDgAv-TgHxKB6W3iucIAo1XWrAbu4A,7009
 gsrap/parsedb/.ipynb_checkpoints/__init__-checkpoint.py,sha256=1k2K1gz4lIdXAwHEdJ0OhdkPu83woGv0Z4TpT1kGrTk,97
-gsrap/parsedb/.ipynb_checkpoints/annotation-checkpoint.py,sha256=-9w1v6pSOJvQfG9BXmUigOFvHQ2qD9FF0EHoRftHiWw,4702
-gsrap/parsedb/.ipynb_checkpoints/completeness-checkpoint.py,sha256=i9QJ_5CU8XmlHEouYo67Uxof7d8QG4imVTdkkAdQe2M,9348
-gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py,sha256=wWhUpmvJJdFyc74RAQrPOmOT3_I6T7ZkATiIU2pglCI,16366
+gsrap/parsedb/.ipynb_checkpoints/annotation-checkpoint.py,sha256=Y02_zXJj_tS1GyBdfuLBy9YJjMgx3mjX6tqr1KhQ-9Q,4810
+gsrap/parsedb/.ipynb_checkpoints/completeness-checkpoint.py,sha256=5P_OxGfKXSJDDV0qIcd6xQvAJymsMQKvhsUvMl79dkk,9478
+gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py,sha256=PuIdXvkF7gmihOEMECXVZ1V4VBOld8p3lZZ2rqXjPH8,16871
 gsrap/parsedb/.ipynb_checkpoints/manual-checkpoint.py,sha256=F16wU8vLyM6V4F611ABuMJtwSAskL5KEgCJ7EQm_F9Y,2177
-gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=nhpL1qVQ-yNcah7KnzS8No6tdNUz0H3cmywu6JCf6y4,7240
-gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py,sha256=fPf9PPjy3wlEnnQJclT9qKRx0YUo2s_c4cBD21_cw_0,5493
+gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=F0vYUvlFkBvg1Jis1nNJ9cS4f3tSF61hbM4zg7D3OJs,7242
+gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py,sha256=9PgsSw-H84eN_dFUwK5FLgbqvydsdic4-VjCrZqkfnY,5703
 gsrap/parsedb/__init__.py,sha256=1k2K1gz4lIdXAwHEdJ0OhdkPu83woGv0Z4TpT1kGrTk,97
-gsrap/parsedb/annotation.py,sha256=-9w1v6pSOJvQfG9BXmUigOFvHQ2qD9FF0EHoRftHiWw,4702
-gsrap/parsedb/completeness.py,sha256=i9QJ_5CU8XmlHEouYo67Uxof7d8QG4imVTdkkAdQe2M,9348
-gsrap/parsedb/introduce.py,sha256=wWhUpmvJJdFyc74RAQrPOmOT3_I6T7ZkATiIU2pglCI,16366
+gsrap/parsedb/annotation.py,sha256=Y02_zXJj_tS1GyBdfuLBy9YJjMgx3mjX6tqr1KhQ-9Q,4810
+gsrap/parsedb/completeness.py,sha256=5P_OxGfKXSJDDV0qIcd6xQvAJymsMQKvhsUvMl79dkk,9478
+gsrap/parsedb/introduce.py,sha256=PuIdXvkF7gmihOEMECXVZ1V4VBOld8p3lZZ2rqXjPH8,16871
 gsrap/parsedb/manual.py,sha256=F16wU8vLyM6V4F611ABuMJtwSAskL5KEgCJ7EQm_F9Y,2177
-gsrap/parsedb/parsedb.py,sha256=nhpL1qVQ-yNcah7KnzS8No6tdNUz0H3cmywu6JCf6y4,7240
-gsrap/parsedb/repeating.py,sha256=fPf9PPjy3wlEnnQJclT9qKRx0YUo2s_c4cBD21_cw_0,5493
+gsrap/parsedb/parsedb.py,sha256=F0vYUvlFkBvg1Jis1nNJ9cS4f3tSF61hbM4zg7D3OJs,7242
+gsrap/parsedb/repeating.py,sha256=9PgsSw-H84eN_dFUwK5FLgbqvydsdic4-VjCrZqkfnY,5703
 gsrap/runsims/.ipynb_checkpoints/__init__-checkpoint.py,sha256=6E6E1gWgH0V7ls4Omx4mxxC85gMJ_27YqhjugJzlZtY,97
 gsrap/runsims/.ipynb_checkpoints/biosynth-checkpoint.py,sha256=fUlHUo4CfB4rGX9Dth87B1p5E5sz7i6spR7ZoqDDGaI,2836
 gsrap/runsims/.ipynb_checkpoints/cnps-checkpoint.py,sha256=A0U8QPqW_uyrtHs99F286aEDEC6eukHXeMWrmnd0efA,5636
@@ -74,7 +74,7 @@ gsrap/runsims/.ipynb_checkpoints/essentialgenes-checkpoint.py,sha256=MzHiuaU1gwi
 gsrap/runsims/.ipynb_checkpoints/growthfactors-checkpoint.py,sha256=r_W4idtOSJBDh7HURRsU8s1TqfOZ3TfeVw2HHDxmnGU,2265
 gsrap/runsims/.ipynb_checkpoints/precursors-checkpoint.py,sha256=1RNt_Rxs0L1lolDmYh4_CiZgiwHfU5B_AcomJO6vJ28,2219
 gsrap/runsims/.ipynb_checkpoints/runsims-checkpoint.py,sha256=2FC5Gs8oSYyZTjHF3A7aXB_O6myVfcn3bCxQfLJlZTk,2842
-gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py,sha256=iHp69_0hAYylICAnuOmjYiYMlC9faKeQsuZVoLaiROo,2378
+gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py,sha256=whNezVUgdTFO5H8_Q6_jo5rM-zyzj17bzGDcrxfTotc,2339
 gsrap/runsims/.ipynb_checkpoints/singleomission-checkpoint.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
 gsrap/runsims/__init__.py,sha256=6E6E1gWgH0V7ls4Omx4mxxC85gMJ_27YqhjugJzlZtY,97
 gsrap/runsims/biosynth.py,sha256=fUlHUo4CfB4rGX9Dth87B1p5E5sz7i6spR7ZoqDDGaI,2836
@@ -83,10 +83,10 @@ gsrap/runsims/essentialgenes.py,sha256=MzHiuaU1gwiPdjZAgG7tkdYzkTTvoNCLp5tkezZhz
 gsrap/runsims/growthfactors.py,sha256=r_W4idtOSJBDh7HURRsU8s1TqfOZ3TfeVw2HHDxmnGU,2265
 gsrap/runsims/precursors.py,sha256=1RNt_Rxs0L1lolDmYh4_CiZgiwHfU5B_AcomJO6vJ28,2219
 gsrap/runsims/runsims.py,sha256=2FC5Gs8oSYyZTjHF3A7aXB_O6myVfcn3bCxQfLJlZTk,2842
-gsrap/runsims/simplegrowth.py,sha256=iHp69_0hAYylICAnuOmjYiYMlC9faKeQsuZVoLaiROo,2378
+gsrap/runsims/simplegrowth.py,sha256=whNezVUgdTFO5H8_Q6_jo5rM-zyzj17bzGDcrxfTotc,2339
 gsrap/runsims/singleomission.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
-gsrap-0.7.0.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gsrap-0.7.0.dist-info/METADATA,sha256=Vra-CI5I5ScraM_w59b8YsLQhXynAHj2-a40Khlm-SA,826
-gsrap-0.7.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-gsrap-0.7.0.dist-info/entry_points.txt,sha256=S9MY0DjfnbKGlZbp5bV7W6dNFy3APoEV84u9x6MV1eI,36
-gsrap-0.7.0.dist-info/RECORD,,
+gsrap-0.7.1.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gsrap-0.7.1.dist-info/METADATA,sha256=ps1z-ZR33q-YL1KeATh-RUNNuB4VU47Mz4OAl2b1F24,826
+gsrap-0.7.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+gsrap-0.7.1.dist-info/entry_points.txt,sha256=S9MY0DjfnbKGlZbp5bV7W6dNFy3APoEV84u9x6MV1eI,36
+gsrap-0.7.1.dist-info/RECORD,,