gsrap 0.8.2__py3-none-any.whl → 0.9.0__py3-none-any.whl

gsrap/parsedb/parsedb.py

@@ -16,7 +16,10 @@ from ..commons import write_excel_model
 from ..commons import show_contributions
 from ..commons import adjust_biomass_precursors
 from ..commons import count_undrawn_rids
+from ..commons import count_undrawn_rids_focus
+
 from ..commons import format_expansion
+from ..commons import check_taxon
 from ..commons import download_keggorg
 from ..commons import initialize_model
 from ..commons import get_memote_results_dict
@@ -46,6 +49,7 @@ from .cycles import verify_egc_all
 def main(args, logger):
     
     
+    ###### FORMAT ARGS NOT REQUIRING RESOURCES
     # adjust out folder path                      
     while args.outdir.endswith('/'):              
         args.outdir = args.outdir[:-1]
@@ -77,17 +81,8 @@ def main(args, logger):
     if args.onlyauthor == '-': args.onlyauthor = None
     
     
-    # format the --eggnog param
-    args.eggnog = format_expansion(logger, args.eggnog)  # now 'args.eggnog' could still be '-'
-    
-    # get the kegg organism if requested
-    if args.keggorg != '-':
-        response = download_keggorg(logger, args.keggorg, args.outdir)
-        if response == 1: return 1
-    
-    
-    
     
+    ###### LOAD LOCAL RESOURCES
     # check and extract the required 'gsrap.maps' file
     if os.path.exists(f'{args.inmaps}') == False:
         logger.error(f"File 'gsrap.maps' not found at {args.inmaps}.")
@@ -108,9 +103,27 @@ def main(args, logger):
             kegg_compound_to_others = pickle.load(handle)
     with resources.path("gsrap.assets", f"kegg_reaction_to_others.pickle") as asset_path: 
         with open(asset_path, 'rb') as handle:
-            kegg_reaction_to_others = pickle.load(handle)   
+            kegg_reaction_to_others = pickle.load(handle) 
+            
+            
+            
+    ###### FORMAT/CHECK FOCUSING ARGS
+    # format the --eggnog param
+    args.eggnog = format_expansion(logger, args.eggnog)  # now 'args.eggnog' could still be '-'
     
+    # check the --taxon param
+    if args.taxon != '-':
+        response = check_taxon(logger, args.taxon, idcollection_dict)
+        if response == 1: return 1
     
+    # get the kegg organism if requested
+    if args.keggorg != '-':
+        response = download_keggorg(logger, args.keggorg, args.outdir)
+        if response == 1: return 1
+    
+    
+    
+    # DOWNLOAD ONLINE RESOURCES
     # get dbuni and dbexp:
     logger.info("Downloading gsrap database...")
     response = get_databases(logger)
@@ -166,14 +179,15 @@ def main(args, logger):
     
     ###### CHECKS 1
     # check universe completness
-    df_C = check_completeness(logger, universe, args.progress, args.module, args.focus, args.eggnog, args.keggorg, idcollection_dict, summary_dict, args.outdir)
+    df_C = check_completeness(logger, universe, args.progress, args.module, args.focus, args.taxon, args.eggnog, args.keggorg, idcollection_dict, summary_dict, args.outdir)
     if type(df_C)==int: return 1
 
 
 
     ###### POLISHING 1
     # remove disconnected metabolites
-    universe = remove_disconnected(logger, universe)
+    if args.keepdisconn == False:
+        universe = remove_disconnected(logger, universe)   # can be commented when using booster.py
 
     
     
@@ -182,9 +196,9 @@ def main(args, logger):
     verify_egc_all(logger, universe, args.outdir)
     
     
+    
     if not args.justparse:
         
-        
         ###### CHECKS 3
         # check growth on minmal media
         df_G = grow_on_media(logger, universe, dbexp, args.media, '-', True)
@@ -217,10 +231,15 @@ def main(args, logger):
 
 
 
-        # output the universe
-        logger.info("Writing universal model...")
-        cobra.io.save_json_model(universe, f'{args.outdir}/universe.json')
-        logger.info(f"'{args.outdir}/universe.json' created!")
+    # output the universe (even when --justparse)
+    logger.info("Writing universal model...")
+    cobra.io.save_json_model(universe, f'{args.outdir}/universe.json')
+    logger.info(f"'{args.outdir}/universe.json' created!")
+    
+    
+    if not args.justparse:
+        
+        # outptu in the remaining formats:
         cobra.io.write_sbml_model(universe, f'{args.outdir}/universe.xml')   # groups are saved only to SBML 
         logger.info(f"'{args.outdir}/universe.xml' created!")
         force_id_on_sbml(f'{args.outdir}/universe.xml', 'universe')   # force introduction of the 'id=""' field
@@ -231,7 +250,9 @@ def main(args, logger):
     
     ###### CHECKS 4
     # check if universal escher map is updated:
-    count_undrawn_rids(logger, universe, lastmap)
+    count_undrawn_rids(logger, universe, lastmap, args.focus)
+    if args.focus != '-':
+        count_undrawn_rids_focus(logger, universe, lastmap, args.focus, args.outdir)
     
     
     return 0

gsrap/parsedb/repeating.py

@@ -45,7 +45,7 @@ def check_gpr(logger, rid, row, kr_ids, idcollection_dict, addtype='R'):
             pass
         elif ko_id not in idcollection_dict['ko'] and ko_id != 'spontaneous' and ko_id != 'orphan':
             logger.error(f"{itemtype} '{rid}' has an invalid KEGG Ortholog: '{ko_id}'.")
-            return 1
+            return 1   # can be commented when migrating to new kegg release
         
         
         # check if these ko_ids are really assigned to this reaction:
@@ -61,7 +61,7 @@ def check_gpr(logger, rid, row, kr_ids, idcollection_dict, addtype='R'):
         missing_ko_ids = ko_for_rid - (set(ko_ids_parsed) - set(['spontaneous', 'orphan']))
         if len(missing_ko_ids) > 0:
             logger.error(f"Orthologs {missing_ko_ids} are missing from reaction '{rid}' ({kr_ids}).")
-            return 1
+            return 1   # can be commented when migrating to new kegg release
             
             
     return 0

{gsrap-0.8.2.dist-info → gsrap-0.9.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: gsrap
-Version: 0.8.2
+Version: 0.9.0
 Summary: 
 License: GNU General Public License v3.0
 Author: Gioele Lazzari

{gsrap-0.8.2.dist-info → gsrap-0.9.0.dist-info}/RECORD

@@ -1,5 +1,5 @@
-gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=o4xMVuraz_Qnf6ZOtxcYjNl-a7-zlRuZsP-GEw8lP4I,15240
-gsrap/__init__.py,sha256=o4xMVuraz_Qnf6ZOtxcYjNl-a7-zlRuZsP-GEw8lP4I,15240
+gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=8or3yeJRjjuaKUSWD5w3-I27LWKUF5hz9ECtzdQ_PKU,15583
+gsrap/__init__.py,sha256=8or3yeJRjjuaKUSWD5w3-I27LWKUF5hz9ECtzdQ_PKU,15583
 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
@@ -9,14 +9,14 @@ gsrap/assets/PM2A.csv,sha256=rjYTdwe8lpRS552BYiUP3J71juG2ywVdR5Sux6fjZTY,8816
 gsrap/assets/PM3B.csv,sha256=42IGX_2O5bRYSiHoMuVKT-T-bzVj0cSRZBvGOrbnQMA,8130
 gsrap/assets/PM4A.csv,sha256=f_5__0Ap_T0KYje5h9veW29I2qB4yU0h7Hr7WpaHjSc,9081
 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/assets/kegg_compound_to_others.pickle,sha256=ddo1bdFSQOSmXJBuvsWWKSsFDWT_XOfV6ZG1BBj4-ew,8498114
+gsrap/assets/kegg_reaction_to_others.pickle,sha256=x53Ch8GjNWXHeqCF5wCPdANmi0ZxmhusYGNfDlk2ZpQ,1582568
 gsrap/commons/.ipynb_checkpoints/__init__-checkpoint.py,sha256=9lrb0sBFSWEgV_e5FYzSgjTbam8b959rW_8VuxQHt1M,268
 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=e-7ffMD4R07MWEgXyGcwjhScbWnG7A3L100YWbpNMk0,8461
-gsrap/commons/.ipynb_checkpoints/escherutils-checkpoint.py,sha256=_y0TgM0-Im0RT8W8z5rr4vlnGK55iRFds6DlDsjGD-8,1151
-gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py,sha256=1KemKQ5oWziFlrT3__70-AKjXwdsqwEzVswEOSbNBDs,11433
+gsrap/commons/.ipynb_checkpoints/downloads-checkpoint.py,sha256=JrVk-UbQzelefGvOz5k4j8Ofib58u_KD_zlUzTcuv6g,11170
+gsrap/commons/.ipynb_checkpoints/escherutils-checkpoint.py,sha256=VQ1FXyby6Cbfw3UNHzRoePH8M8owJ8E2rzB-11vBweA,3732
+gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py,sha256=_LtaWripY_D99f14Yk-3v9VIov2cUGzJ53AXgmNFpUk,11457
 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
@@ -28,9 +28,9 @@ gsrap/commons/.ipynb_checkpoints/sbmlutils-checkpoint.py,sha256=gkY02qbGXrbYStn2
 gsrap/commons/__init__.py,sha256=9lrb0sBFSWEgV_e5FYzSgjTbam8b959rW_8VuxQHt1M,268
 gsrap/commons/biomass.py,sha256=4u7WBaUgo42tBoXDU1D0VUjICatb44e0jfswZrBeHYs,17987
 gsrap/commons/coeffs.py,sha256=qI3_GuqHkeA2KbK9pYdkqJaFwYemAVZJGLRR4QtHt6w,19182
-gsrap/commons/downloads.py,sha256=e-7ffMD4R07MWEgXyGcwjhScbWnG7A3L100YWbpNMk0,8461
-gsrap/commons/escherutils.py,sha256=_y0TgM0-Im0RT8W8z5rr4vlnGK55iRFds6DlDsjGD-8,1151
-gsrap/commons/excelhub.py,sha256=1KemKQ5oWziFlrT3__70-AKjXwdsqwEzVswEOSbNBDs,11433
+gsrap/commons/downloads.py,sha256=JrVk-UbQzelefGvOz5k4j8Ofib58u_KD_zlUzTcuv6g,11170
+gsrap/commons/escherutils.py,sha256=VQ1FXyby6Cbfw3UNHzRoePH8M8owJ8E2rzB-11vBweA,3732
+gsrap/commons/excelhub.py,sha256=_LtaWripY_D99f14Yk-3v9VIov2cUGzJ53AXgmNFpUk,11457
 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
@@ -40,11 +40,11 @@ gsrap/commons/memoteutils.py,sha256=rulJFSVX4I-XGi4uHXloL0eGIkC5zhpuJYWJn9zCDbY,
 gsrap/commons/metrics.py,sha256=gvqF2c0e31m5qQWQ11JF4-eMqxtuONy_7lUiC7uaXX4,3291
 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=BFAbBZFp-yaT35XO38YFHRqQr4mSAfRH6unOrPenQus,2703
-gsrap/getmaps/.ipynb_checkpoints/kdown-checkpoint.py,sha256=mv5wqP4DX9KhB1IIWx6cLrc-MjQdF5Nz-Gii8QSO_6I,24498
+gsrap/getmaps/.ipynb_checkpoints/getmaps-checkpoint.py,sha256=5Odf2PS1PmPZqQyKoLPYHYgNvYsp6IxrTy5HEQ5LNEM,2943
+gsrap/getmaps/.ipynb_checkpoints/kdown-checkpoint.py,sha256=OZGeGdnXMLzxvitwMTWKYZyL4dq3T8ZqbT4HVC3F3lI,27452
 gsrap/getmaps/__init__.py,sha256=L4gLwk1vgnPlQuIP-FPnvy9uXnmGVQ4Rvjv3uyciDfk,92
-gsrap/getmaps/getmaps.py,sha256=BFAbBZFp-yaT35XO38YFHRqQr4mSAfRH6unOrPenQus,2703
-gsrap/getmaps/kdown.py,sha256=mv5wqP4DX9KhB1IIWx6cLrc-MjQdF5Nz-Gii8QSO_6I,24498
+gsrap/getmaps/getmaps.py,sha256=5Odf2PS1PmPZqQyKoLPYHYgNvYsp6IxrTy5HEQ5LNEM,2943
+gsrap/getmaps/kdown.py,sha256=OZGeGdnXMLzxvitwMTWKYZyL4dq3T8ZqbT4HVC3F3lI,27452
 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
@@ -60,21 +60,21 @@ gsrap/mkmodel/mkmodel.py,sha256=zm-JA2sXwqTLalCc0L5POw2iRI56QK0UJMUgorHQrLw,1083
 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=Y02_zXJj_tS1GyBdfuLBy9YJjMgx3mjX6tqr1KhQ-9Q,4810
-gsrap/parsedb/.ipynb_checkpoints/completeness-checkpoint.py,sha256=yhFiEslK1qmMCk_GWZ7UZtX02FUqLU39UafG5886WsY,12016
+gsrap/parsedb/.ipynb_checkpoints/annotation-checkpoint.py,sha256=r0sYkSqA6b8mZOGD1tgk7I__ZFkH8r4aqxVA6EUspEY,5205
+gsrap/parsedb/.ipynb_checkpoints/completeness-checkpoint.py,sha256=IziYv6xShUnKVxnHUwJ_I2TfiKplSXoiHQoUakI1xFI,13141
 gsrap/parsedb/.ipynb_checkpoints/cycles-checkpoint.py,sha256=HJ58LcHQseQ1eploysfXd5Y8Rip8n62qhje4pmL22VM,4761
 gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py,sha256=UuwGWGB2saG9VDMoboumeRBWhHOO68bs5_1r2RSkyVo,17145
-gsrap/parsedb/.ipynb_checkpoints/manual-checkpoint.py,sha256=qMKYshVftSGCRAjHC87E6n9-6kAiffFFCgHOUbqlyC0,3625
-gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=fTZlQvjV_wyRIxWJbW5TCVvydn0-CsYknsx9FYspdu8,8127
-gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py,sha256=WwPOzlZgsZWmJ-rvhFg21iOJ6gajgKFc2vCIHh6weBg,6103
+gsrap/parsedb/.ipynb_checkpoints/manual-checkpoint.py,sha256=sDux5CFNC8v2YJ3oDMV0vXsQrvSG6gov1f4hftc4nyo,3874
+gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=HbjkcWRI916_pvKVwTruNUbRWrHRlT__200wocLSOMY,8860
+gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py,sha256=ph1gC-84SyBnBuM7s0A9jTJBJmBlRzq0lk4FYG70228,6215
 gsrap/parsedb/__init__.py,sha256=1k2K1gz4lIdXAwHEdJ0OhdkPu83woGv0Z4TpT1kGrTk,97
-gsrap/parsedb/annotation.py,sha256=Y02_zXJj_tS1GyBdfuLBy9YJjMgx3mjX6tqr1KhQ-9Q,4810
-gsrap/parsedb/completeness.py,sha256=yhFiEslK1qmMCk_GWZ7UZtX02FUqLU39UafG5886WsY,12016
+gsrap/parsedb/annotation.py,sha256=r0sYkSqA6b8mZOGD1tgk7I__ZFkH8r4aqxVA6EUspEY,5205
+gsrap/parsedb/completeness.py,sha256=IziYv6xShUnKVxnHUwJ_I2TfiKplSXoiHQoUakI1xFI,13141
 gsrap/parsedb/cycles.py,sha256=HJ58LcHQseQ1eploysfXd5Y8Rip8n62qhje4pmL22VM,4761
 gsrap/parsedb/introduce.py,sha256=UuwGWGB2saG9VDMoboumeRBWhHOO68bs5_1r2RSkyVo,17145
-gsrap/parsedb/manual.py,sha256=qMKYshVftSGCRAjHC87E6n9-6kAiffFFCgHOUbqlyC0,3625
-gsrap/parsedb/parsedb.py,sha256=fTZlQvjV_wyRIxWJbW5TCVvydn0-CsYknsx9FYspdu8,8127
-gsrap/parsedb/repeating.py,sha256=WwPOzlZgsZWmJ-rvhFg21iOJ6gajgKFc2vCIHh6weBg,6103
+gsrap/parsedb/manual.py,sha256=8UCvfMK7HSXd_-JlnIWgMmBnsFGojTGE63iOJE5J_6E,3884
+gsrap/parsedb/parsedb.py,sha256=HbjkcWRI916_pvKVwTruNUbRWrHRlT__200wocLSOMY,8860
+gsrap/parsedb/repeating.py,sha256=ph1gC-84SyBnBuM7s0A9jTJBJmBlRzq0lk4FYG70228,6215
 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=2FC5Gs8oSYyZTjHF3A7aXB_O6myVfcn3bCxQfLJlZTk,2842
 gsrap/runsims/simplegrowth.py,sha256=tCQHTMUqum1YwlBKRTNaQoag2co_yQlCaKmISOARAlE,2353
 gsrap/runsims/singleomission.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
-gsrap-0.8.2.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gsrap-0.8.2.dist-info/METADATA,sha256=CEZpXejZ1b_KWKhxPbSXKGdW01ZU_nkKFqzfafDXXGE,898
-gsrap-0.8.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-gsrap-0.8.2.dist-info/entry_points.txt,sha256=S9MY0DjfnbKGlZbp5bV7W6dNFy3APoEV84u9x6MV1eI,36
-gsrap-0.8.2.dist-info/RECORD,,
+gsrap-0.9.0.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gsrap-0.9.0.dist-info/METADATA,sha256=Zd_nRZYHhrKBle7mzTBWnQQ1KdMWlHPuKqH9-YU5IHA,898
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+gsrap-0.9.0.dist-info/entry_points.txt,sha256=S9MY0DjfnbKGlZbp5bV7W6dNFy3APoEV84u9x6MV1eI,36
+gsrap-0.9.0.dist-info/RECORD,,