gsrap 0.7.2__py3-none-any.whl → 0.8.1__py3-none-any.whl

gsrap/parsedb/introduce.py

@@ -143,6 +143,14 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
             m.annotation[ankey] = list(m.annotation[ankey])
             
             
+        # replace inchikey with manually-curated
+        if m.annotation['inchikey'] != [] and m.annotation['inchikey'] != [row['inchikey']]:
+            logger.debug(f"Metabolite '{pure_mid}': manual-curated inchikey ({[row['inchikey']]}) is diferent from the one derived from MNX ({m.annotation['inchikey']}).")
+        m.annotation['inchikey'] = [row['inchikey']]  # force the manual-curated version
+        if m.annotation['inchikey'] == ['XXXXXXXXXXXXXX-XXXXXXXXXX-X']:
+            m.annotation['inchikey'] = []
+            
+            
         # add SBO annotation
         m.annotation['sbo'] = ['SBO:0000247']  # generic metabolite
    
@@ -279,15 +287,7 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
         r = model.reactions.get_by_id(f'EX_{mid_e}')
         r.name = f"Exchange for {model.metabolites.get_by_id(mid_e).name}"
         r.build_reaction_from_string(f'{mid_e} --> ')
-        if mid_e in [
-            # basics:
-            'glc__D_e', 'nh4_e', 'pi_e', 'so4_e', 'h2o_e', 'h_e', 'o2_e', 'co2_e',
-            # metals: 
-            'cu2_e', 'mobd_e', 'fe2_e', 'cobalt2_e',
-        ]:
-            r.bounds = (-1000, 1000)
-        else:
-            r.bounds = (0, 1000)
+        r.bounds = (0, 1000)
             
         # add SBO annotation
         r.annotation['sbo'] = ['SBO:0000627']  # exchange reaction    

gsrap/parsedb/manual.py

@@ -19,6 +19,33 @@ def get_rids_with_mancheck_gpr():
     return rids_mancheck_gpr
 
 
+def get_rids_with_mancheck_balancing():
+    rids_mancheck_bal = [  # same reactions involving ATP can be reversible
+        
+        # SECTION "reversible both in KEGG and MetaCyc"
+        'PGK', 'SUCOAS', 'ADK1', 'GK1', 'NNATr', 'CYTK1', 'ACKr',
+        'DGK1', 'PPAKr', 'ATPSr', 'NDPK10',
+        
+        ### SECTION "reversible in KEGG but not in MetaCyc" ###
+        'CYTK2',  # clearly reversible in KEGG but not in MetaCyc (RXN-7913)
+        'DADK',  # clearly reversible in KEGG but not in MetaCyc (DEOXYADENYLATE-KINASE-RXN)
+        'UMPK',  # clearly reversible in KEGG but not in MetaCyc (RXN-12002)
+        'NDPK1',  # clearly reversible in KEGG but not in MetaCyc (GDPKIN-RXN)
+        'NDPK2',  # clearly reversible in KEGG but not in MetaCyc (UDPKIN-RXN)  
+        'NDPK3',  # clearly reversible in KEGG but not in MetaCyc (CDPKIN-RXN)
+        'NDPK4',  # clearly reversible in KEGG but not in MetaCyc (DTDPKIN-RXN)
+        'NDPK5',  # clearly reversible in KEGG but not in MetaCyc (DGDPKIN-RXN)
+        'NDPK6',  # clearly reversible in KEGG but not in MetaCyc (DUDPKIN-RXN)
+        'NDPK7',  # clearly reversible in KEGG but not in MetaCyc (DCDPKIN-RXN)
+        'NDPK8',  # clearly reversible in KEGG but not in MetaCyc (DADPKIN-RXN)
+        'NDPK9',  # clearly reversible in KEGG but not in MetaCyc (RXN-14120) 
+        
+        ### SECTION "missing reversibility info" ###
+        'LPHERA',  
+    ]
+    return rids_mancheck_bal
+
+
 
 def get_manual_sinks():
     

gsrap/parsedb/parsedb.py

@@ -17,6 +17,7 @@ from ..commons import show_contributions
 from ..commons import adjust_biomass_precursors
 from ..commons import count_undrawn_rids
 from ..commons import format_expansion
+from ..commons import download_keggorg
 
 from .introduce import introduce_metabolites
 from .introduce import introduce_reactions
@@ -34,6 +35,8 @@ from ..runsims.biosynth import biosynthesis_on_media
 
 from ..mkmodel.polishing import remove_disconnected
 
+from .cycles import verify_egc_all
+
 
 
 
@@ -72,7 +75,14 @@ def main(args, logger):
     
     
     # format the --eggnog param
-    args.eggnog = format_expansion(logger, args.eggnog)
+    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
+    
+    
     
     
     # check and extract the required 'gsrap.maps' file
@@ -153,7 +163,7 @@ def main(args, logger):
     
     ###### CHECKS 1
     # check universe completness
-    df_C = check_completeness(logger, universe, args.progress, args.module, args.focus, args.eggnog, idcollection_dict, summary_dict)
+    df_C = check_completeness(logger, universe, args.progress, args.module, args.focus, args.eggnog, args.keggorg, idcollection_dict, summary_dict, args.outdir)
     if type(df_C)==int: return 1
 
 
@@ -165,6 +175,9 @@ def main(args, logger):
     
     
     ###### CHECKS 2
+    # check erroneous EGCs
+    verify_egc_all(logger, universe, args.outdir)
+    
     # check growth on minmal media
     df_G = grow_on_media(logger, universe, dbexp, args.media, '-', True)
     if type(df_G)==int: return 1

gsrap/parsedb/repeating.py

@@ -4,6 +4,7 @@ import cobra
 
 from .manual import get_deprecated_kos
 from .manual import get_rids_with_mancheck_gpr
+from .manual import get_rids_with_mancheck_balancing
 
 
 
@@ -138,6 +139,14 @@ def add_reaction(logger, model, rid, row, kr_ids, kegg_reaction_to_others, addty
         return 1    
     
     
+    # check if reversible and using ATP
+    if r.lower_bound < 0 and r.upper_bound > 0:
+        for m in r.metabolites: 
+            if m.id.rsplit('_', 1)[0] == 'atp':
+                if rid not in get_rids_with_mancheck_balancing():
+                    logger.warning(f"Reaction '{rid}' involves ATP and is reversible: are you sure?")
+    
+    
     return 0
 
 

{gsrap-0.7.2.dist-info → gsrap-0.8.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: gsrap
-Version: 0.7.2
+Version: 0.8.1
 Summary: 
 License: GNU General Public License v3.0
 Author: Gioele Lazzari

{gsrap-0.7.2.dist-info → gsrap-0.8.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
-gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=nTCojQmYOSv1tRDBEZu7p2Ne_jB9xTUEIylln19tHkk,13818
-gsrap/__init__.py,sha256=nTCojQmYOSv1tRDBEZu7p2Ne_jB9xTUEIylln19tHkk,13818
+gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=lOurIE_Gn0jYS3ks3UmX11uuMrMScHADH9ivFoLpg5k,14160
+gsrap/__init__.py,sha256=lOurIE_Gn0jYS3ks3UmX11uuMrMScHADH9ivFoLpg5k,14160
 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
@@ -11,28 +11,30 @@ 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/commons/.ipynb_checkpoints/__init__-checkpoint.py,sha256=P_rdjFcL_FjkKYT3a0IJiQTzWL7p2Hm6z-hjuCZEHgU,216
+gsrap/commons/.ipynb_checkpoints/__init__-checkpoint.py,sha256=QuHINLSWNb0XKagHRWXzU5UVxw3ECTncvR7llRKblso,241
 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
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-gsrap/commons/.ipynb_checkpoints/figures-checkpoint.py,sha256=qIjyMMFrm7AkUkdYY4ZZ8SjprUfoC3brW34oHRQvNQk,3689
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+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=VYKN8X1PNERP6uQDbznZXfgflLEvnw4j1T8AIAdrE7s,2902
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 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/__init__.py,sha256=QuHINLSWNb0XKagHRWXzU5UVxw3ECTncvR7llRKblso,241
 gsrap/commons/biomass.py,sha256=4u7WBaUgo42tBoXDU1D0VUjICatb44e0jfswZrBeHYs,17987
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 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=VYKN8X1PNERP6uQDbznZXfgflLEvnw4j1T8AIAdrE7s,2902
+gsrap/commons/medium.py,sha256=wcWiuZ-mqryoYBrsIHkIen6fBssR_1FGVoXUTApylNc,2901
 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
@@ -45,30 +47,32 @@ gsrap/mkmodel/.ipynb_checkpoints/__init__-checkpoint.py,sha256=PNze-26HMOwfdJ92K
 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=S6nFUZ1Bbdf13nVJhGK2S5C_V3hd5zwTg2o5nzejngg,3123
-gsrap/mkmodel/.ipynb_checkpoints/mkmodel-checkpoint.py,sha256=5dW5eAKW9iAFlPITM-0ZjL2FmFp3OTSvLI-xbJ-zGgs,8550
+gsrap/mkmodel/.ipynb_checkpoints/mkmodel-checkpoint.py,sha256=3o4_B3ALcq6GYLAZ7zteNOcLTfE3KVJO6s9L4uMmw8E,10448
 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/.ipynb_checkpoints/pruner-checkpoint.py,sha256=FAZid-0H6j66wR2dVKRAaMaDREVt1edflmZXbX7blXg,9836
 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=S6nFUZ1Bbdf13nVJhGK2S5C_V3hd5zwTg2o5nzejngg,3123
-gsrap/mkmodel/mkmodel.py,sha256=5dW5eAKW9iAFlPITM-0ZjL2FmFp3OTSvLI-xbJ-zGgs,8550
+gsrap/mkmodel/mkmodel.py,sha256=3o4_B3ALcq6GYLAZ7zteNOcLTfE3KVJO6s9L4uMmw8E,10448
 gsrap/mkmodel/polishing.py,sha256=R1UdFPxN8N27Iu0jsYW2N_1BkWEbBHaMYW6NkCYZK_k,3256
-gsrap/mkmodel/pruner.py,sha256=BVOK1iFXpTgZswDgAv-TgHxKB6W3iucIAo1XWrAbu4A,7009
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 gsrap/parsedb/__init__.py,sha256=1k2K1gz4lIdXAwHEdJ0OhdkPu83woGv0Z4TpT1kGrTk,97
 gsrap/parsedb/annotation.py,sha256=Y02_zXJj_tS1GyBdfuLBy9YJjMgx3mjX6tqr1KhQ-9Q,4810
-gsrap/parsedb/completeness.py,sha256=mLK2YawP9FjR3yogHhGxF2b2ti9DKmLu9uhibsq0jy4,11064
-gsrap/parsedb/introduce.py,sha256=PuIdXvkF7gmihOEMECXVZ1V4VBOld8p3lZZ2rqXjPH8,16871
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-gsrap/parsedb/parsedb.py,sha256=tTWohNPIrw47a08ECFTyHuT4W5KlkznllIEBCpg7Kv0,7169
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+gsrap/parsedb/manual.py,sha256=qMKYshVftSGCRAjHC87E6n9-6kAiffFFCgHOUbqlyC0,3625
+gsrap/parsedb/parsedb.py,sha256=M44zFmaYu50LYDjFH3IdiezjPbzuDIzZ9ukzwU4ZBBM,7583
+gsrap/parsedb/repeating.py,sha256=WwPOzlZgsZWmJ-rvhFg21iOJ6gajgKFc2vCIHh6weBg,6103
 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
@@ -87,8 +91,8 @@ 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
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