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

gsrap/parsedb/parsedb.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/repeating.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-0.10.1.dist-info → gsrap-0.10.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: gsrap
-Version: 0.10.1
+Version: 0.10.2
 Summary: 
 License: GNU General Public License v3.0
 License-File: LICENSE.txt
@@ -27,5 +27,5 @@ Requires-Dist: pandas (>=2.0.0)
 Requires-Dist: xlsxwriter (>=3.1.0)
 Description-Content-Type: text/markdown
 
-Source code for `gsrap`.
+Source code for `gsrap`. 
 

{gsrap-0.10.1.dist-info → gsrap-0.10.2.dist-info}/RECORD

@@ -1,5 +1,5 @@
-gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=OIblfpgppQI7PgC7Or9D4AmLsihTRdiuMUsGs2iiJ_A,15624
-gsrap/__init__.py,sha256=OIblfpgppQI7PgC7Or9D4AmLsihTRdiuMUsGs2iiJ_A,15624
+gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=IgLF196hShcOLmStzW-h_kFykSe1lrKjlO_LIvBKkDU,16210
+gsrap/__init__.py,sha256=IgLF196hShcOLmStzW-h_kFykSe1lrKjlO_LIvBKkDU,16210
 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
@@ -12,32 +12,32 @@ gsrap/assets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 gsrap/assets/kegg_compound_to_others.pickle,sha256=BPjrr8Gmlqqj1ufCT_lWLmDJaZ0Iu8f_XS7KJU_gLck,8498114
 gsrap/assets/kegg_reaction_to_others.pickle,sha256=Gh4ANppTm_ZW-Hn-YE8EG87fMPt3EIVXk2YMZBerKqA,1763940
 gsrap/commons/.ipynb_checkpoints/__init__-checkpoint.py,sha256=9lrb0sBFSWEgV_e5FYzSgjTbam8b959rW_8VuxQHt1M,268
-gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py,sha256=eJ2lej72mjDAibS7lQCFfN-L4inkaQ3lERe7K6-1E5o,18059
-gsrap/commons/.ipynb_checkpoints/coeffs-checkpoint.py,sha256=qI3_GuqHkeA2KbK9pYdkqJaFwYemAVZJGLRR4QtHt6w,19182
-gsrap/commons/.ipynb_checkpoints/downloads-checkpoint.py,sha256=UKgFSPkxuxVWXoqrtZXEF42RR_KUjyoo_9wpCL-19X8,15908
-gsrap/commons/.ipynb_checkpoints/escherutils-checkpoint.py,sha256=4xtFsR-DDFsrYoDC6FIGZuLxQPLfNHoaE92RlnilunI,3747
+gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py,sha256=2NdDJ-jt9W-KOCXjfjIWByoK1MeLbXq3ovNNUjjS-es,18060
+gsrap/commons/.ipynb_checkpoints/coeffs-checkpoint.py,sha256=uCN8yxsIQ7pgWSx0_A1lZ0c_MWGM1hfANyC7EAoIvls,19183
+gsrap/commons/.ipynb_checkpoints/downloads-checkpoint.py,sha256=KH5HxcIJPD06ZQ3iiiglnmryP0XK8uzbgE7Xm6u7IcQ,15912
+gsrap/commons/.ipynb_checkpoints/escherutils-checkpoint.py,sha256=VkflnQfoknz5m721yiRVnBBdVihmZAHGF4eJbCbszCg,9681
 gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py,sha256=h0TNzbjUiUQfXQrl7GRZlSc16GRzSRg3GJuwz9cXK78,11735
 gsrap/commons/.ipynb_checkpoints/figures-checkpoint.py,sha256=IRHSQXrCi4SQoISEfNB0rDhvUzbjcgsPi9zUSefsRto,4316
 gsrap/commons/.ipynb_checkpoints/fluxbal-checkpoint.py,sha256=jgC3-vI9Tbjvqohh2mJwFra4rl_pbUzHWrSa_QAxVO4,1262
 gsrap/commons/.ipynb_checkpoints/keggutils-checkpoint.py,sha256=M2nhHRiNH_xObHSxOIdt7ix59MrPdl9q3HNICC8X36M,4514
 gsrap/commons/.ipynb_checkpoints/logutils-checkpoint.py,sha256=VsnrkIsUftS3MOOwAd0n0peQ7a2X5ZEx930eCtzmW7g,1317
-gsrap/commons/.ipynb_checkpoints/medium-checkpoint.py,sha256=AMj95IvyWpbqKAYW5QdG_pyFXHDllUZ-b8dAsPR7tvU,3859
+gsrap/commons/.ipynb_checkpoints/medium-checkpoint.py,sha256=025g33eev3NTEYVCAIcE0LYMM5uZkvrPMJRI2pYfLKk,3860
 gsrap/commons/.ipynb_checkpoints/memoteutils-checkpoint.py,sha256=rulJFSVX4I-XGi4uHXloL0eGIkC5zhpuJYWJn9zCDbY,4981
-gsrap/commons/.ipynb_checkpoints/metrics-checkpoint.py,sha256=yosbgX_EWUujN3AT6joY4xNxxJI97Qk3C0aKwko_mXs,3297
+gsrap/commons/.ipynb_checkpoints/metrics-checkpoint.py,sha256=H-ya8HELdsh2onNmSgYmIFuyg0jpcf-9cp0VkZ6paqk,3314
 gsrap/commons/.ipynb_checkpoints/sbmlutils-checkpoint.py,sha256=gkY02qbGXrbYStn2F8J0KM0fmqati2Nbvi128EF7coI,365
 gsrap/commons/__init__.py,sha256=9lrb0sBFSWEgV_e5FYzSgjTbam8b959rW_8VuxQHt1M,268
-gsrap/commons/biomass.py,sha256=eJ2lej72mjDAibS7lQCFfN-L4inkaQ3lERe7K6-1E5o,18059
-gsrap/commons/coeffs.py,sha256=qI3_GuqHkeA2KbK9pYdkqJaFwYemAVZJGLRR4QtHt6w,19182
-gsrap/commons/downloads.py,sha256=UKgFSPkxuxVWXoqrtZXEF42RR_KUjyoo_9wpCL-19X8,15908
-gsrap/commons/escherutils.py,sha256=4xtFsR-DDFsrYoDC6FIGZuLxQPLfNHoaE92RlnilunI,3747
+gsrap/commons/biomass.py,sha256=2NdDJ-jt9W-KOCXjfjIWByoK1MeLbXq3ovNNUjjS-es,18060
+gsrap/commons/coeffs.py,sha256=uCN8yxsIQ7pgWSx0_A1lZ0c_MWGM1hfANyC7EAoIvls,19183
+gsrap/commons/downloads.py,sha256=KH5HxcIJPD06ZQ3iiiglnmryP0XK8uzbgE7Xm6u7IcQ,15912
+gsrap/commons/escherutils.py,sha256=VkflnQfoknz5m721yiRVnBBdVihmZAHGF4eJbCbszCg,9681
 gsrap/commons/excelhub.py,sha256=h0TNzbjUiUQfXQrl7GRZlSc16GRzSRg3GJuwz9cXK78,11735
 gsrap/commons/figures.py,sha256=IRHSQXrCi4SQoISEfNB0rDhvUzbjcgsPi9zUSefsRto,4316
 gsrap/commons/fluxbal.py,sha256=jgC3-vI9Tbjvqohh2mJwFra4rl_pbUzHWrSa_QAxVO4,1262
 gsrap/commons/keggutils.py,sha256=M2nhHRiNH_xObHSxOIdt7ix59MrPdl9q3HNICC8X36M,4514
 gsrap/commons/logutils.py,sha256=VsnrkIsUftS3MOOwAd0n0peQ7a2X5ZEx930eCtzmW7g,1317
-gsrap/commons/medium.py,sha256=AMj95IvyWpbqKAYW5QdG_pyFXHDllUZ-b8dAsPR7tvU,3859
+gsrap/commons/medium.py,sha256=025g33eev3NTEYVCAIcE0LYMM5uZkvrPMJRI2pYfLKk,3860
 gsrap/commons/memoteutils.py,sha256=rulJFSVX4I-XGi4uHXloL0eGIkC5zhpuJYWJn9zCDbY,4981
-gsrap/commons/metrics.py,sha256=yosbgX_EWUujN3AT6joY4xNxxJI97Qk3C0aKwko_mXs,3297
+gsrap/commons/metrics.py,sha256=H-ya8HELdsh2onNmSgYmIFuyg0jpcf-9cp0VkZ6paqk,3314
 gsrap/commons/sbmlutils.py,sha256=gkY02qbGXrbYStn2F8J0KM0fmqati2Nbvi128EF7coI,365
 gsrap/getmaps/.ipynb_checkpoints/__init__-checkpoint.py,sha256=L4gLwk1vgnPlQuIP-FPnvy9uXnmGVQ4Rvjv3uyciDfk,92
 gsrap/getmaps/.ipynb_checkpoints/getmaps-checkpoint.py,sha256=5Odf2PS1PmPZqQyKoLPYHYgNvYsp6IxrTy5HEQ5LNEM,2943
@@ -60,21 +60,21 @@ gsrap/mkmodel/mkmodel.py,sha256=k_HZMmFTaJnXxjjk9nWCX5m1VyAXyNAM0S5h69wi-PM,1084
 gsrap/mkmodel/polishing.py,sha256=R1UdFPxN8N27Iu0jsYW2N_1BkWEbBHaMYW6NkCYZK_k,3256
 gsrap/mkmodel/pruner.py,sha256=FAZid-0H6j66wR2dVKRAaMaDREVt1edflmZXbX7blXg,9836
 gsrap/parsedb/.ipynb_checkpoints/__init__-checkpoint.py,sha256=1k2K1gz4lIdXAwHEdJ0OhdkPu83woGv0Z4TpT1kGrTk,97
-gsrap/parsedb/.ipynb_checkpoints/annotation-checkpoint.py,sha256=uJIU653LzAH3n1HGuT_MnnyTgspMeMZztGQMOw3FH2w,6005
+gsrap/parsedb/.ipynb_checkpoints/annotation-checkpoint.py,sha256=EbafgDhLfued7z0AW_LUdR5fkwSoXZt7fJN13d-EVtE,6535
 gsrap/parsedb/.ipynb_checkpoints/completeness-checkpoint.py,sha256=LKldz8Y4cl6LvUECzgvnufhlS8GlpOwK3M8j3dPYjwc,13197
 gsrap/parsedb/.ipynb_checkpoints/cycles-checkpoint.py,sha256=HJ58LcHQseQ1eploysfXd5Y8Rip8n62qhje4pmL22VM,4761
-gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py,sha256=2mSl9zbRLjH4MslVb6_idWM8oqGbAQvGA9j2wjhmvAE,19641
+gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py,sha256=VJeEZFNSrCzCVofcgO2l-R4RRdk-yRTZbYYVqG595JA,19694
 gsrap/parsedb/.ipynb_checkpoints/manual-checkpoint.py,sha256=lrVR3ftABzLHrWvY-tp0LZe2k1FniSYRjQztd5J840A,5452
-gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=zUfDJANj7USbsD1bMK6QIriXxF66IrEs0yWGHk3pKlE,8859
-gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py,sha256=_v9IFfjfZ4WJfGir2-iMJ_BADwwcOidXl0-I8stEtOE,7084
+gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=iYzVmoHn0bWqLwTAjm8rsNd02__fHZjFAVg2WaJmJI0,9162
+gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py,sha256=Yz3slRPleyU0ixG934ebhKhVHdnd1sDS0HFSluk144k,7097
 gsrap/parsedb/__init__.py,sha256=1k2K1gz4lIdXAwHEdJ0OhdkPu83woGv0Z4TpT1kGrTk,97
-gsrap/parsedb/annotation.py,sha256=uJIU653LzAH3n1HGuT_MnnyTgspMeMZztGQMOw3FH2w,6005
+gsrap/parsedb/annotation.py,sha256=EbafgDhLfued7z0AW_LUdR5fkwSoXZt7fJN13d-EVtE,6535
 gsrap/parsedb/completeness.py,sha256=LKldz8Y4cl6LvUECzgvnufhlS8GlpOwK3M8j3dPYjwc,13197
 gsrap/parsedb/cycles.py,sha256=HJ58LcHQseQ1eploysfXd5Y8Rip8n62qhje4pmL22VM,4761
-gsrap/parsedb/introduce.py,sha256=2mSl9zbRLjH4MslVb6_idWM8oqGbAQvGA9j2wjhmvAE,19641
+gsrap/parsedb/introduce.py,sha256=VJeEZFNSrCzCVofcgO2l-R4RRdk-yRTZbYYVqG595JA,19694
 gsrap/parsedb/manual.py,sha256=lrVR3ftABzLHrWvY-tp0LZe2k1FniSYRjQztd5J840A,5452
-gsrap/parsedb/parsedb.py,sha256=zUfDJANj7USbsD1bMK6QIriXxF66IrEs0yWGHk3pKlE,8859
-gsrap/parsedb/repeating.py,sha256=_v9IFfjfZ4WJfGir2-iMJ_BADwwcOidXl0-I8stEtOE,7084
+gsrap/parsedb/parsedb.py,sha256=iYzVmoHn0bWqLwTAjm8rsNd02__fHZjFAVg2WaJmJI0,9162
+gsrap/parsedb/repeating.py,sha256=Yz3slRPleyU0ixG934ebhKhVHdnd1sDS0HFSluk144k,7097
 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
@@ -93,8 +93,8 @@ gsrap/runsims/precursors.py,sha256=1RNt_Rxs0L1lolDmYh4_CiZgiwHfU5B_AcomJO6vJ28,2
 gsrap/runsims/runsims.py,sha256=aVELI1re1Dlm1_Lh7t1DwSoA8AcxQw0JKNnjV9w5F20,2910
 gsrap/runsims/simplegrowth.py,sha256=rVN69v4B-DdxOJDsJ_JOVzbnWsDYafMq43QD_GJIpjs,2296
 gsrap/runsims/singleomission.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
-gsrap-0.10.1.dist-info/METADATA,sha256=AGbAQL3AEB3s3o9-jmWHZoVsjZQXRyUKVfQQlbWUitA,1008
-gsrap-0.10.1.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
-gsrap-0.10.1.dist-info/entry_points.txt,sha256=S9MY0DjfnbKGlZbp5bV7W6dNFy3APoEV84u9x6MV1eI,36
-gsrap-0.10.1.dist-info/licenses/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gsrap-0.10.1.dist-info/RECORD,,
+gsrap-0.10.2.dist-info/METADATA,sha256=VWxCnsgKP3EHy3Fljh08nqJnyyzYP2lprdbhXX3xK38,1009
+gsrap-0.10.2.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
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+gsrap-0.10.2.dist-info/licenses/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gsrap-0.10.2.dist-info/RECORD,,