gsrap 0.10.1__py3-none-any.whl → 0.10.2__py3-none-any.whl

gsrap/commons/metrics.py

@@ -58,8 +58,8 @@ def show_contributions(logger, db, goodbefore):
         return 0
     
     
-    # create a counter for each author
-    cnt = {author: 0 for author in db['curators']['username']}
+    # create a counter for each curator
+    cnt = {curator: 0 for curator in db['curators']['username']}
     cnt_tot = 0
     
     
@@ -67,9 +67,9 @@ def show_contributions(logger, db, goodbefore):
         if type(row['curator']) != str: 
             logger.error(f"Missing curator in tab 'R', rid '{row['rid']}'.")
             return 1
-        for author in row['curator'].split(';'):
-            author = author.rstrip().strip()
-            cnt[author] += 1
+        for curator in row['curator'].split(';'):
+            curator = curator.rstrip().strip()
+            cnt[curator] += 1
             cnt_tot += 1
             
             
@@ -77,18 +77,18 @@ def show_contributions(logger, db, goodbefore):
         if type(row['curator']) != str: 
             logger.error(f"Missing curator in tab 'T', rid '{row['rid']}'.")
             return 1
-        for author in row['curator'].split(';'):
-            author = author.rstrip().strip()
-            cnt[author] += 1
+        for curator in row['curator'].split(';'):
+            curator = curator.rstrip().strip()
+            cnt[curator] += 1
             cnt_tot += 1
         
         
     # compute percentages:
-    pct = {author: cnt[author]/cnt_tot*100 for author in cnt.keys()}
+    pct = {curator: cnt[curator]/cnt_tot*100 for curator in cnt.keys()}
     # sort in descending order: 
     pct = dict(sorted(pct.items(), key=lambda item: item[1], reverse=True))
     # convert to string:
-    pct = {author: f'{round(pct[author],2)}%' for author in pct.keys()}
+    pct = {curator: f'{round(pct[curator],2)}%' for curator in pct.keys()}
     logger.debug(f"Contributions: {pct}.")
     
     

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

@@ -1,4 +1,5 @@
 import threading
+import copy
 
 import cobra
 
@@ -106,7 +107,7 @@ def translate_annotate_genes(logger, model, idcollection_dict):
     
 
 
-def set_up_groups(logger, model, idcollection_dict):
+def set_up_groups(logger, model, idcollection_dict, goodbefore):
     
     
     logger.debug("Introducing groups...")
@@ -160,18 +161,27 @@ def set_up_groups(logger, model, idcollection_dict):
         model.add_groups([actual_group])
         
         
-        
-    # insert custom groups:
-    custom_groups = get_custom_groups()
-    #
     # create a group for transporters on-the-fly
+    custom_groups = get_custom_groups()
     custom_groups['gr_transport'] = []
     for r in model.reactions:
         if len(r.metabolites) == 1 and list(r.metabolites)[0].id.rsplit('_',1)[-1] != 'c':  # just exchanges (esclude sinks/demands)
             custom_groups['gr_transport'].append(r.id)
         if len(set([m.id.rsplit('_', 1)[-1] for m in r.metabolites])) > 1:  # transport reactions
             custom_groups['gr_transport'].append(r.id)
-    #
+    
+    
+    # handle eventual removed reactions as consequence of --goodbefore:
+    if type(goodbefore) == list:
+        modeled_rids = [r.id for r in model.reactions]
+        for group_id in custom_groups.keys():
+            for rid in copy.deepcopy(custom_groups[group_id]):
+                if rid not in modeled_rids:
+                    logger.warning(f"Removing reaction '{rid}' from group '{group_id}' as consequence of --goodbefore.")
+                    custom_groups[group_id].remove(rid)
+        
+        
+    # actually insert custom groups:
     for group_id in custom_groups.keys():
         actual_group = cobra.core.Group(
             group_id, 

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

@@ -3,7 +3,7 @@ import sys
 import pandas as pnd
 import cobra
 
-from .repeating import check_author
+from .repeating import check_curator
 from .repeating import check_rstring_arrow
 from .repeating import check_gpr
 from .repeating import add_reaction
@@ -14,7 +14,7 @@ from .manual import get_manual_demands
 
 
     
-def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to_others, outdir, goodbefore, onlyauthor):
+def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to_others, outdir, goodbefore, onlycurator):
     goodbefore_reached = False
     
     
@@ -44,24 +44,24 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
             goodbefore_reached = True
             
             
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor == None:
+            if onlycurator == None:
                 logger.warning(f"Skipping metabolite '{pure_mid}' as requested with --goodbefore[0] '{goodbefore}'.")
                 continue
         
         
         # parse and get curators
-        response = check_author(logger, pure_mid, row, db, 'M')
+        response = check_curator(logger, pure_mid, row, db, 'M')
         if type(response) == int: return 1
-        else: authors = response
+        else: curators = response
         
         
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor != None and onlyauthor not in authors:
-                authors_string = '; '.join(authors)
-                logger.warning(f"Skipping metabolite '{pure_mid}' (authors '{authors_string}') as requested with --goodbefore[0] '{goodbefore}' and --onlyauthor '{onlyauthor}'.")
+            if onlycurator != None and onlycurator not in curators:
+                curators_string = '; '.join(curators)
+                logger.warning(f"Skipping metabolite '{pure_mid}' (curators '{curators_string}') as requested with --goodbefore[0] '{goodbefore}' and --onlycurator '{onlycurator}'.")
                 continue
             
         
@@ -122,7 +122,7 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
                         eqbiggids.add(eqbiggid)
         if pure_mid not in eqbiggids and eqbiggids != set():
             with open(f"{outdir}/logs/M.inbigg.txt", 'a') as f:
-                print(f"Metabolites '{'; '.join(kc_ids)}' already in BiGG as {eqbiggids} ({authors} gave '{pure_mid}').", file=f)        
+                print(f"Metabolites '{'; '.join(kc_ids)}' already in BiGG as {eqbiggids} ({curators} gave '{pure_mid}').", file=f)        
         
         
         # add metabolite to model
@@ -136,7 +136,7 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
         
         
         # write curators as annotations
-        m.annotation['curator_codes'] = authors
+        m.annotation['curator_codes'] = curators
         
         
         # add annotations to model (same order of Memote)
@@ -197,7 +197,7 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
     
     
     
-def introduce_reactions(logger, db, model, idcollection_dict, kegg_reaction_to_others, outdir, goodbefore, onlyauthor): 
+def introduce_reactions(logger, db, model, idcollection_dict, kegg_reaction_to_others, outdir, goodbefore, onlycurator): 
     goodbefore_reached = False
     
     
@@ -226,24 +226,24 @@ def introduce_reactions(logger, db, model, idcollection_dict, kegg_reaction_to_o
             goodbefore_reached = True
         
         
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor == None:
+            if onlycurator == None:
                 logger.warning(f"Skipping reaction '{rid}' as requested with --goodbefore[1] '{goodbefore}'.")
                 continue
         
         
         # parse and get curators
-        response = check_author(logger, rid, row, db, 'R')
+        response = check_curator(logger, rid, row, db, 'R')
         if type(response) == int: return 1
-        else: authors = response
+        else: curators = response
                     
                     
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor != None and onlyauthor not in authors:
-                authors_string = '; '.join(authors)
-                logger.warning(f"Skipping reaction '{rid}' (authors '{authors_string}') as requested with --goodbefore[1] '{goodbefore}' and --onlyauthor '{onlyauthor}'.")
+            if onlycurator != None and onlycurator not in curators:
+                curators_string = '; '.join(curators)
+                logger.warning(f"Skipping reaction '{rid}' (curators '{curators_string}') as requested with --goodbefore[1] '{goodbefore}' and --onlycurator '{onlycurator}'.")
                 continue
         
         
@@ -284,11 +284,11 @@ def introduce_reactions(logger, db, model, idcollection_dict, kegg_reaction_to_o
                         eqbiggids.add(eqbiggid)
         if rid not in eqbiggids and eqbiggids != set():
             with open(f"{outdir}/logs/R.inbigg.txt", 'a') as f:
-                print(f"Reactions '{'; '.join(kr_ids)}' already in BiGG as {eqbiggids} ({authors} gave '{rid}').", file=f) 
+                print(f"Reactions '{'; '.join(kr_ids)}' already in BiGG as {eqbiggids} ({curators} gave '{rid}').", file=f) 
         
         
         # add reaction to model
-        response = add_reaction(logger, model, rid, authors, row, kr_ids, kegg_reaction_to_others, 'R', outdir)
+        response = add_reaction(logger, model, rid, curators, row, kr_ids, kegg_reaction_to_others, 'R', outdir)
         if response == 1: return 1
     
     
@@ -308,7 +308,7 @@ def introduce_reactions(logger, db, model, idcollection_dict, kegg_reaction_to_o
       
     
     
-def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_to_others, outdir, goodbefore, onlyauthor): 
+def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_to_others, outdir, goodbefore, onlycurator): 
     goodbefore_reached = False
     
     
@@ -373,24 +373,24 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
             return 1
             
             
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor == None:
+            if onlycurator == None:
                 logger.warning(f"Skipping transport '{rid}' as requested with --goodbefore[2] '{goodbefore}'.")
                 continue
         
         
-        # parse author
-        response = check_author(logger, rid, row, db, 'T')
+        # parse curator
+        response = check_curator(logger, rid, row, db, 'T')
         if type(response) == int: return 1
-        else: authors = response
+        else: curators = response
                     
                     
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor != None and onlyauthor not in authors:
-                authors_string = '; '.join(authors)
-                logger.warning(f"Skipping transport '{rid}' (authors '{authors_string}') as requested with --goodbefore[2] '{goodbefore}' and --onlyauthor '{onlyauthor}'.")
+            if onlycurator != None and onlycurator not in curators:
+                curators_string = '; '.join(curators)
+                logger.warning(f"Skipping transport '{rid}' (curators '{curators_string}') as requested with --goodbefore[2] '{goodbefore}' and --onlycurator '{onlycurator}'.")
                 continue
         
         
@@ -454,11 +454,11 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
                         eqbiggids.add(eqbiggid)
         if rid not in eqbiggids and eqbiggids != set():
             with open(f"{outdir}/logs/T.inbigg.txt", 'a') as f:
-                print(f"Reactions '{'; '.join(kr_ids)}' already in BiGG as {eqbiggids} ({authors} gave '{rid}').", file=f) 
+                print(f"Reactions '{'; '.join(kr_ids)}' already in BiGG as {eqbiggids} ({curators} gave '{rid}').", file=f) 
                     
                     
         # add reaction to model
-        response = add_reaction(logger, model, rid, authors, row, kr_ids, kegg_reaction_to_others, 'T', outdir)
+        response = add_reaction(logger, model, rid, curators, row, kr_ids, kegg_reaction_to_others, 'T', outdir)
         if response == 1: return 1
         rids_parsed.append(rid)   # update list of rids in model
         

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

@@ -17,7 +17,7 @@ from ..commons import write_excel_model
 from ..commons import show_contributions
 from ..commons import adjust_biomass_precursors
 from ..commons import count_undrawn_rids_focus
-
+from ..commons import parse_zipped_escher
 from ..commons import format_expansion
 from ..commons import check_taxon
 from ..commons import download_keggorg
@@ -50,6 +50,9 @@ def main(args, logger):
     
     
     
+    
+    
+    
     ###### PRE-PARSING
     
     # adjust out folder path                      
@@ -72,9 +75,9 @@ def main(args, logger):
         return 1
     
     
-    # check 'goodbefore' and 'onlyauthor' params
-    if args.goodbefore == '-' and args.onlyauthor != '-':
-        logger.error(f"--onlyauthor must be used in conjunction with --goodbefore.")
+    # check 'goodbefore' and 'onlycurator' params
+    if args.goodbefore == '-' and args.onlycurator != '-':
+        logger.error(f"--onlycurator must be used in conjunction with --goodbefore.")
         return 1
     if   args.goodbefore == '-': args.goodbefore = [None, None, None]
     elif len(args.goodbefore.split('-')) != 3: 
@@ -85,7 +88,7 @@ def main(args, logger):
         if args.goodbefore[0] == 'None': args.goodbefore[0] = None
         if args.goodbefore[1] == 'None': args.goodbefore[1] = None
         if args.goodbefore[2] == 'None': args.goodbefore[2] = None
-    if args.onlyauthor == '-': args.onlyauthor = None
+    if args.onlycurator == '-': args.onlycurator = None
     
     
     # check and extract the required 'gsrap.maps' file
@@ -147,17 +150,17 @@ def main(args, logger):
     
     
     # introduce M 
-    universe = introduce_metabolites(logger, dbuni, universe, idcollection_dict, kegg_compound_to_others, args.outdir, args.goodbefore[0], args.onlyauthor)
+    universe = introduce_metabolites(logger, dbuni, universe, idcollection_dict, kegg_compound_to_others, args.outdir, args.goodbefore[0], args.onlycurator)
     if type(universe)==int: return 1
 
 
     # introduce R
-    universe = introduce_reactions(logger, dbuni, universe, idcollection_dict, kegg_reaction_to_others, args.outdir, args.goodbefore[1], args.onlyauthor)
+    universe = introduce_reactions(logger, dbuni, universe, idcollection_dict, kegg_reaction_to_others, args.outdir, args.goodbefore[1], args.onlycurator)
     if type(universe)==int: return 1
 
 
     # introduce T
-    universe = introduce_transporters(logger, dbuni, universe, idcollection_dict, kegg_reaction_to_others, args.outdir, args.goodbefore[2], args.onlyauthor)
+    universe = introduce_transporters(logger, dbuni, universe, idcollection_dict, kegg_reaction_to_others, args.outdir, args.goodbefore[2], args.onlycurator)
     if type(universe)==int: return 1
 
 
@@ -177,10 +180,16 @@ def main(args, logger):
 
 
     # introduce collections (groups of Rs as maps/modules)
-    universe = set_up_groups(logger, universe, idcollection_dict)
+    universe = set_up_groups(logger, universe, idcollection_dict, args.goodbefore)
     if type(universe)==int: return 1
 
 
+    # introduce hand-drwn escher map annotation
+    if args.escherzip != '-':
+        universe = parse_zipped_escher(logger, universe, args.escherzip, args.outdir)
+        if type(universe) == int: return 1
+
+
     
     ###### POST-PARSING
     
@@ -199,7 +208,7 @@ def main(args, logger):
 
     # remove disconnected metabolites
     if args.keepdisconn == False:
-        universe = remove_disconnected(logger, universe)   # can be commented when using booster.py
+        universe = remove_disconnected(logger, universe)   # keep disconnected metabolites when using booster.py
 
     
     # avoid time-consuming activities

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

@@ -1,7 +1,6 @@
 import pandas as pnd
 import cobra
 
-
 from .manual import get_deprecated_kos
 from .manual import get_rids_with_mancheck_gpr
 from .manual import get_rids_with_mancheck_balancing
@@ -90,7 +89,7 @@ def check_rstring_arrow(logger, rid, row, addtype='R'):
 
 
 
-def check_author(logger, mrid, row, db, addtype='R'): 
+def check_curator(logger, mrid, row, db, addtype='R'): 
     
     
     # define itemtype:
@@ -101,23 +100,23 @@ def check_author(logger, mrid, row, db, addtype='R'):
     else: itemtype = 'Transporter'
     
     
-    # check if author was indicated:
+    # check if curator was indicated:
     if pnd.isna(row['curator']): 
         logger.error(f"{itemtype} '{mrid}' has no curator.")
         return 1
     
     
-    # check if the are valid authors
-    authors = set()
-    for author in row['curator'].split(';'):
-        author = author.strip()
-        authors.add(author)
-        if author not in db['curators']['username'].to_list(): 
-            logger.error(f"{itemtype} '{mrid}' has invalid curator: '{author}'.")
+    # check if the are valid curators
+    curators = set()
+    for curator in row['curator'].split(';'):
+        curator = curator.strip()
+        curators.add(curator)
+        if curator not in db['curators']['username'].to_list(): 
+            logger.error(f"{itemtype} '{mrid}' has invalid curator: '{curator}'.")
             return 1
     
     
-    return list(authors)
+    return list(curators)
     
     
     
@@ -137,7 +136,7 @@ def get_curator_notes(logger, row):
     
     
     
-def add_reaction(logger, model, rid, authors, row, kr_ids, kegg_reaction_to_others, addtype, outdir):
+def add_reaction(logger, model, rid, curators, row, kr_ids, kegg_reaction_to_others, addtype, outdir):
     
     
     # define the itemtype:
@@ -180,7 +179,7 @@ def add_reaction(logger, model, rid, authors, row, kr_ids, kegg_reaction_to_othe
         
         
     # write curators as annotations
-    r.annotation['curator_codes'] = authors
+    r.annotation['curator_codes'] = curators
         
     
     # add annotations to model (same order of Memote)

gsrap/parsedb/annotation.py

@@ -1,4 +1,5 @@
 import threading
+import copy
 
 import cobra
 
@@ -106,7 +107,7 @@ def translate_annotate_genes(logger, model, idcollection_dict):
     
 
 
-def set_up_groups(logger, model, idcollection_dict):
+def set_up_groups(logger, model, idcollection_dict, goodbefore):
     
     
     logger.debug("Introducing groups...")
@@ -160,18 +161,27 @@ def set_up_groups(logger, model, idcollection_dict):
         model.add_groups([actual_group])
         
         
-        
-    # insert custom groups:
-    custom_groups = get_custom_groups()
-    #
     # create a group for transporters on-the-fly
+    custom_groups = get_custom_groups()
     custom_groups['gr_transport'] = []
     for r in model.reactions:
         if len(r.metabolites) == 1 and list(r.metabolites)[0].id.rsplit('_',1)[-1] != 'c':  # just exchanges (esclude sinks/demands)
             custom_groups['gr_transport'].append(r.id)
         if len(set([m.id.rsplit('_', 1)[-1] for m in r.metabolites])) > 1:  # transport reactions
             custom_groups['gr_transport'].append(r.id)
-    #
+    
+    
+    # handle eventual removed reactions as consequence of --goodbefore:
+    if type(goodbefore) == list:
+        modeled_rids = [r.id for r in model.reactions]
+        for group_id in custom_groups.keys():
+            for rid in copy.deepcopy(custom_groups[group_id]):
+                if rid not in modeled_rids:
+                    logger.warning(f"Removing reaction '{rid}' from group '{group_id}' as consequence of --goodbefore.")
+                    custom_groups[group_id].remove(rid)
+        
+        
+    # actually insert custom groups:
     for group_id in custom_groups.keys():
         actual_group = cobra.core.Group(
             group_id, 

gsrap/parsedb/introduce.py

@@ -3,7 +3,7 @@ import sys
 import pandas as pnd
 import cobra
 
-from .repeating import check_author
+from .repeating import check_curator
 from .repeating import check_rstring_arrow
 from .repeating import check_gpr
 from .repeating import add_reaction
@@ -14,7 +14,7 @@ from .manual import get_manual_demands
 
 
     
-def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to_others, outdir, goodbefore, onlyauthor):
+def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to_others, outdir, goodbefore, onlycurator):
     goodbefore_reached = False
     
     
@@ -44,24 +44,24 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
             goodbefore_reached = True
             
             
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor == None:
+            if onlycurator == None:
                 logger.warning(f"Skipping metabolite '{pure_mid}' as requested with --goodbefore[0] '{goodbefore}'.")
                 continue
         
         
         # parse and get curators
-        response = check_author(logger, pure_mid, row, db, 'M')
+        response = check_curator(logger, pure_mid, row, db, 'M')
         if type(response) == int: return 1
-        else: authors = response
+        else: curators = response
         
         
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor != None and onlyauthor not in authors:
-                authors_string = '; '.join(authors)
-                logger.warning(f"Skipping metabolite '{pure_mid}' (authors '{authors_string}') as requested with --goodbefore[0] '{goodbefore}' and --onlyauthor '{onlyauthor}'.")
+            if onlycurator != None and onlycurator not in curators:
+                curators_string = '; '.join(curators)
+                logger.warning(f"Skipping metabolite '{pure_mid}' (curators '{curators_string}') as requested with --goodbefore[0] '{goodbefore}' and --onlycurator '{onlycurator}'.")
                 continue
             
         
@@ -122,7 +122,7 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
                         eqbiggids.add(eqbiggid)
         if pure_mid not in eqbiggids and eqbiggids != set():
             with open(f"{outdir}/logs/M.inbigg.txt", 'a') as f:
-                print(f"Metabolites '{'; '.join(kc_ids)}' already in BiGG as {eqbiggids} ({authors} gave '{pure_mid}').", file=f)        
+                print(f"Metabolites '{'; '.join(kc_ids)}' already in BiGG as {eqbiggids} ({curators} gave '{pure_mid}').", file=f)        
         
         
         # add metabolite to model
@@ -136,7 +136,7 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
         
         
         # write curators as annotations
-        m.annotation['curator_codes'] = authors
+        m.annotation['curator_codes'] = curators
         
         
         # add annotations to model (same order of Memote)
@@ -197,7 +197,7 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
     
     
     
-def introduce_reactions(logger, db, model, idcollection_dict, kegg_reaction_to_others, outdir, goodbefore, onlyauthor): 
+def introduce_reactions(logger, db, model, idcollection_dict, kegg_reaction_to_others, outdir, goodbefore, onlycurator): 
     goodbefore_reached = False
     
     
@@ -226,24 +226,24 @@ def introduce_reactions(logger, db, model, idcollection_dict, kegg_reaction_to_o
             goodbefore_reached = True
         
         
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor == None:
+            if onlycurator == None:
                 logger.warning(f"Skipping reaction '{rid}' as requested with --goodbefore[1] '{goodbefore}'.")
                 continue
         
         
         # parse and get curators
-        response = check_author(logger, rid, row, db, 'R')
+        response = check_curator(logger, rid, row, db, 'R')
         if type(response) == int: return 1
-        else: authors = response
+        else: curators = response
                     
                     
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor != None and onlyauthor not in authors:
-                authors_string = '; '.join(authors)
-                logger.warning(f"Skipping reaction '{rid}' (authors '{authors_string}') as requested with --goodbefore[1] '{goodbefore}' and --onlyauthor '{onlyauthor}'.")
+            if onlycurator != None and onlycurator not in curators:
+                curators_string = '; '.join(curators)
+                logger.warning(f"Skipping reaction '{rid}' (curators '{curators_string}') as requested with --goodbefore[1] '{goodbefore}' and --onlycurator '{onlycurator}'.")
                 continue
         
         
@@ -284,11 +284,11 @@ def introduce_reactions(logger, db, model, idcollection_dict, kegg_reaction_to_o
                         eqbiggids.add(eqbiggid)
         if rid not in eqbiggids and eqbiggids != set():
             with open(f"{outdir}/logs/R.inbigg.txt", 'a') as f:
-                print(f"Reactions '{'; '.join(kr_ids)}' already in BiGG as {eqbiggids} ({authors} gave '{rid}').", file=f) 
+                print(f"Reactions '{'; '.join(kr_ids)}' already in BiGG as {eqbiggids} ({curators} gave '{rid}').", file=f) 
         
         
         # add reaction to model
-        response = add_reaction(logger, model, rid, authors, row, kr_ids, kegg_reaction_to_others, 'R', outdir)
+        response = add_reaction(logger, model, rid, curators, row, kr_ids, kegg_reaction_to_others, 'R', outdir)
         if response == 1: return 1
     
     
@@ -308,7 +308,7 @@ def introduce_reactions(logger, db, model, idcollection_dict, kegg_reaction_to_o
       
     
     
-def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_to_others, outdir, goodbefore, onlyauthor): 
+def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_to_others, outdir, goodbefore, onlycurator): 
     goodbefore_reached = False
     
     
@@ -373,24 +373,24 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
             return 1
             
             
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor == None:
+            if onlycurator == None:
                 logger.warning(f"Skipping transport '{rid}' as requested with --goodbefore[2] '{goodbefore}'.")
                 continue
         
         
-        # parse author
-        response = check_author(logger, rid, row, db, 'T')
+        # parse curator
+        response = check_curator(logger, rid, row, db, 'T')
         if type(response) == int: return 1
-        else: authors = response
+        else: curators = response
                     
                     
-        # manage goodbefore/onlyauthor
+        # manage goodbefore/onlycurator
         if goodbefore != None and goodbefore_reached:
-            if onlyauthor != None and onlyauthor not in authors:
-                authors_string = '; '.join(authors)
-                logger.warning(f"Skipping transport '{rid}' (authors '{authors_string}') as requested with --goodbefore[2] '{goodbefore}' and --onlyauthor '{onlyauthor}'.")
+            if onlycurator != None and onlycurator not in curators:
+                curators_string = '; '.join(curators)
+                logger.warning(f"Skipping transport '{rid}' (curators '{curators_string}') as requested with --goodbefore[2] '{goodbefore}' and --onlycurator '{onlycurator}'.")
                 continue
         
         
@@ -454,11 +454,11 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
                         eqbiggids.add(eqbiggid)
         if rid not in eqbiggids and eqbiggids != set():
             with open(f"{outdir}/logs/T.inbigg.txt", 'a') as f:
-                print(f"Reactions '{'; '.join(kr_ids)}' already in BiGG as {eqbiggids} ({authors} gave '{rid}').", file=f) 
+                print(f"Reactions '{'; '.join(kr_ids)}' already in BiGG as {eqbiggids} ({curators} gave '{rid}').", file=f) 
                     
                     
         # add reaction to model
-        response = add_reaction(logger, model, rid, authors, row, kr_ids, kegg_reaction_to_others, 'T', outdir)
+        response = add_reaction(logger, model, rid, curators, row, kr_ids, kegg_reaction_to_others, 'T', outdir)
         if response == 1: return 1
         rids_parsed.append(rid)   # update list of rids in model