gsrap 0.8.1__py3-none-any.whl → 0.8.3__py3-none-any.whl

gsrap/mkmodel/mkmodel.py

@@ -41,8 +41,12 @@ from ..commons import log_unbalances
 from ..commons import format_expansion
 from ..commons import comparative_table
 from ..commons import download_keggorg
+from ..commons import initialize_model
+from ..commons import get_memote_results_dict
+
 
 from ..runsims.biosynth import biosynthesis_on_media
+from ..runsims.simplegrowth import grow_on_media
 
 from ..parsedb.cycles import verify_egc_all
 
@@ -103,7 +107,7 @@ def create_model_incore(params):
 
     ###### GAPFILLING
     # force inclusion of reactions:  
-    include_forced(logger, model, universe, args.force_inclusion)
+    include_forced(logger, model, universe, args.include)
 
     # remove missing conditional precursors + get the 'cond_col_dict' dict.
     # 'cond_col_dict' is str-to-str: {'pheme_c': 'M00868: 1/8; M00121: 2/12;', 'hemeO_c': 'gr_HemeO: 0/1'}
@@ -114,15 +118,15 @@ def create_model_incore(params):
     if response == 1: return 1
 
     # gap-fill based on media:
-    df_B = gapfill_on_media(logger, model, universe, dbexp, args.gap_fill, cond_col_dict, args.exclude_orphans)
+    df_B = gapfill_on_media(logger, model, universe, dbexp, args.gapfill, cond_col_dict, args.excludeorp)
     if type(df_B)==int: return 1
 
     # force removal of reactions
-    setattr(args, 'force_removal', '-')  # experimental feature, not public. It's main purpose was to test gap-filling in biolog_on_media().
-    remove_forced(logger, model, universe, args.force_removal)
+    setattr(args, 'remove', '-')  # experimental feature, not public. It's main purpose was to test gap-filling in biolog_on_media().
+    remove_forced(logger, model, universe, args.remove)
 
     # perform Biolog(R) curation based on media
-    df_P = biolog_on_media(logger, model, universe, dbexp, args.gap_fill, args.biolog, args.exclude_orphans, args.cnps)
+    df_P = biolog_on_media(logger, model, universe, dbexp, args.gapfill, args.biolog, args.excludeorp, args.cnps)
     if type(df_P)==int: return 1
 
 
@@ -142,12 +146,12 @@ def create_model_incore(params):
 
 
     
-    ###### CHECKS
+    ###### CHECKS 1
     # check erroneous EGCs
     verify_egc_all(logger, model, args.outdir)
     
     # check blocked metabolites / dead-ends
-    df_S = biosynthesis_on_media(logger, model, dbexp, args.gap_fill, args.biosynth)
+    df_S = biosynthesis_on_media(logger, model, dbexp, args.gapfill, args.biosynth)
     if type(df_S)==int: return 1
 
 
@@ -155,6 +159,16 @@ def create_model_incore(params):
     ###### POLISHING 3
     # reset growth environment befor saving the model
     gempipe.reset_growth_env(model)
+    
+    # initialize model
+    response = initialize_model(logger, model, dbexp, args.initialize, args.gapfill)
+    if response==1: return 1
+
+
+
+    ###### CHECKS 2
+    # compute Memote metrics
+    memote_results_dict = get_memote_results_dict(logger, model)
 
 
     
@@ -165,7 +179,7 @@ def create_model_incore(params):
     cobra.io.write_sbml_model(model, f'{args.outdir}/{model.id}.xml')        # SBML   # groups are saved only to SBML
     logger.info(f"'{args.outdir}/{model.id}.xml' created!")
     force_id_on_sbml(f'{args.outdir}/{model.id}.xml', model.id)   # force introduction of the 'id=""' field
-    sheets_dict = write_excel_model(model, f'{args.outdir}/{model.id}.mkmodel.xlsx', args.nofigs, None, df_B, df_P, df_S)  
+    sheets_dict = write_excel_model(model, f'{args.outdir}/{model.id}.mkmodel.xlsx', args.nofigs, memote_results_dict, None, df_B, df_P, df_S)  
     logger.info(f"'{args.outdir}/{model.id}.mkmodel.xlsx' created!")
         
         

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

@@ -27,9 +27,8 @@ def parse_eggnog(model, eggnog, idcollection_dict):
             
             
     # PART 2. get reactions in the organism (even the GPR is not complete)
-    kr_to_kos = idcollection_dict['kr_to_kos']
     krs_org = set()
-    for kr, kos in kr_to_kos.items(): 
+    for kr, kos in idcollection_dict['kr_to_kos'].items(): 
         if any([ko in kos_org for ko in kos]):
             krs_org.add(kr)
     
@@ -49,9 +48,34 @@ def parse_keggorg(keggorg, outdir, idcollection_dict):
     
     
     # PART 2. get reactions in the organism (even the GPR is not complete)
-    kr_to_kos = idcollection_dict['kr_to_kos']
     krs_org = set()
-    for kr, kos in kr_to_kos.items(): 
+    for kr, kos in idcollection_dict['kr_to_kos'].items(): 
+        if any([ko in kos_org for ko in kos]):
+            krs_org.add(kr)
+    
+    
+    return krs_org
+
+
+
+def parse_taxon(taxon, idcollection_dict):
+    
+    
+    # formatting of --taxon was already verified at startup.
+    # also the presence of 'ko_to_taxa' in idcollection_dict was veryfied at startup.
+    level, name = taxon.split(':')
+           
+        
+    # PART 1. get KO codes available
+    kos_org = set()
+    for ko in idcollection_dict['ko_to_taxa'].keys():
+        if name in idcollection_dict['ko_to_taxa'][ko][level]:
+            kos_org.add(ko)
+            
+    
+    # PART 2. get reactions in the organism (even the GPR is not complete)
+    krs_org = set()
+    for kr, kos in idcollection_dict['kr_to_kos'].items(): 
         if any([ko in kos_org for ko in kos]):
             krs_org.add(kr)
     
@@ -60,7 +84,7 @@ def parse_keggorg(keggorg, outdir, idcollection_dict):
 
     
     
-def check_completeness(logger, model, progress, module, focus, eggnog, keggorg, idcollection_dict, summary_dict, outdir): 
+def check_completeness(logger, model, progress, module, focus, taxon, eggnog, keggorg, idcollection_dict, summary_dict, outdir): 
     # check KEGG annotations in the universe model to get '%' of completeness per pathway/module.
     
             
@@ -69,6 +93,9 @@ def check_completeness(logger, model, progress, module, focus, eggnog, keggorg,
     if keggorg != '-':  # keggorg has precedence
         kr_uni = parse_keggorg(keggorg, outdir, idcollection_dict)
         kr_uni_label = f"organism code '{keggorg}'"
+    elif taxon != '-':
+        kr_uni = parse_taxon(taxon, idcollection_dict)
+        kr_uni_label = f"taxon '{taxon}'"
     elif eggnog != '-':
         for eggfile in eggnog:
             eggset = parse_eggnog(model, eggfile, idcollection_dict)

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

@@ -17,7 +17,11 @@ 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 check_taxon
 from ..commons import download_keggorg
+from ..commons import initialize_model
+from ..commons import get_memote_results_dict
+
 
 from .introduce import introduce_metabolites
 from .introduce import introduce_reactions
@@ -43,6 +47,7 @@ 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]
@@ -74,17 +79,8 @@ 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}.")
@@ -105,9 +101,27 @@ 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)
@@ -163,7 +177,7 @@ 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
 
 
@@ -178,41 +192,56 @@ def main(args, logger):
     # 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
     
-    # check blocked biomass precursors
-    cond_col_dict = adjust_biomass_precursors(logger, universe, universe, 1.0)
-    df_E = precursors_on_media(logger, universe, universe, dbexp, args.media, cond_col_dict, args.precursors)
-    if type(df_E)==int: return 1
+    if not args.justparse:
+        
+        
+        ###### CHECKS 3
+        # check growth on minmal media
+        df_G = grow_on_media(logger, universe, dbexp, args.media, '-', True)
+        if type(df_G)==int: return 1
 
-    # check blocked metabolites / dead-ends
-    df_S = biosynthesis_on_media(logger, universe, dbexp, args.media, args.biosynth)
-    if type(df_S)==int: return 1
+        # check blocked biomass precursors
+        cond_col_dict = adjust_biomass_precursors(logger, universe, universe, 1.0)
+        df_E = precursors_on_media(logger, universe, universe, dbexp, args.media, cond_col_dict, args.precursors)
+        if type(df_E)==int: return 1
+
+        # check blocked metabolites / dead-ends
+        df_S = biosynthesis_on_media(logger, universe, dbexp, args.media, args.biosynth)
+        if type(df_S)==int: return 1
 
 
     
-    ###### POLISHING 2
-    # reset growth environment befor saving the model
-    gempipe.reset_growth_env(universe)
-    
+        ###### POLISHING 2
+        # reset growth environment befor saving the model
+        gempipe.reset_growth_env(universe)
+
+        # initialize model
+        response = initialize_model(logger, universe, dbexp, args.initialize, args.media)
+        if response==1: return 1
+
+
+
+        ###### CHECKS 4
+        # compute Memote metrics
+        memote_results_dict = get_memote_results_dict(logger, universe)
+
 
 
-    # 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!")
-    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
-    sheets_dict = write_excel_model(universe, f'{args.outdir}/universe.parsedb.xlsx', args.nofigs, df_E, None, None, df_S, df_C)  
-    logger.info(f"'{args.outdir}/universe.parsedb.xlsx' created!")
+        # 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!")
+        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
+        sheets_dict = write_excel_model(universe, f'{args.outdir}/universe.parsedb.xlsx', args.nofigs, memote_results_dict, df_E, None, None, df_S, df_C)  
+        logger.info(f"'{args.outdir}/universe.parsedb.xlsx' created!")
 
 
     
-    ###### CHECKS 3
-    # check if universal escher map os updated:
+    ###### CHECKS 4
+    # check if universal escher map is updated:
     count_undrawn_rids(logger, universe, lastmap)
     
     

gsrap/parsedb/completeness.py

@@ -27,9 +27,8 @@ def parse_eggnog(model, eggnog, idcollection_dict):
             
             
     # PART 2. get reactions in the organism (even the GPR is not complete)
-    kr_to_kos = idcollection_dict['kr_to_kos']
     krs_org = set()
-    for kr, kos in kr_to_kos.items(): 
+    for kr, kos in idcollection_dict['kr_to_kos'].items(): 
         if any([ko in kos_org for ko in kos]):
             krs_org.add(kr)
     
@@ -49,9 +48,34 @@ def parse_keggorg(keggorg, outdir, idcollection_dict):
     
     
     # PART 2. get reactions in the organism (even the GPR is not complete)
-    kr_to_kos = idcollection_dict['kr_to_kos']
     krs_org = set()
-    for kr, kos in kr_to_kos.items(): 
+    for kr, kos in idcollection_dict['kr_to_kos'].items(): 
+        if any([ko in kos_org for ko in kos]):
+            krs_org.add(kr)
+    
+    
+    return krs_org
+
+
+
+def parse_taxon(taxon, idcollection_dict):
+    
+    
+    # formatting of --taxon was already verified at startup.
+    # also the presence of 'ko_to_taxa' in idcollection_dict was veryfied at startup.
+    level, name = taxon.split(':')
+           
+        
+    # PART 1. get KO codes available
+    kos_org = set()
+    for ko in idcollection_dict['ko_to_taxa'].keys():
+        if name in idcollection_dict['ko_to_taxa'][ko][level]:
+            kos_org.add(ko)
+            
+    
+    # PART 2. get reactions in the organism (even the GPR is not complete)
+    krs_org = set()
+    for kr, kos in idcollection_dict['kr_to_kos'].items(): 
         if any([ko in kos_org for ko in kos]):
             krs_org.add(kr)
     
@@ -60,7 +84,7 @@ def parse_keggorg(keggorg, outdir, idcollection_dict):
 
     
     
-def check_completeness(logger, model, progress, module, focus, eggnog, keggorg, idcollection_dict, summary_dict, outdir): 
+def check_completeness(logger, model, progress, module, focus, taxon, eggnog, keggorg, idcollection_dict, summary_dict, outdir): 
     # check KEGG annotations in the universe model to get '%' of completeness per pathway/module.
     
             
@@ -69,6 +93,9 @@ def check_completeness(logger, model, progress, module, focus, eggnog, keggorg,
     if keggorg != '-':  # keggorg has precedence
         kr_uni = parse_keggorg(keggorg, outdir, idcollection_dict)
         kr_uni_label = f"organism code '{keggorg}'"
+    elif taxon != '-':
+        kr_uni = parse_taxon(taxon, idcollection_dict)
+        kr_uni_label = f"taxon '{taxon}'"
     elif eggnog != '-':
         for eggfile in eggnog:
             eggset = parse_eggnog(model, eggfile, idcollection_dict)

gsrap/parsedb/parsedb.py

@@ -17,7 +17,11 @@ 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 check_taxon
 from ..commons import download_keggorg
+from ..commons import initialize_model
+from ..commons import get_memote_results_dict
+
 
 from .introduce import introduce_metabolites
 from .introduce import introduce_reactions
@@ -43,6 +47,7 @@ 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]
@@ -74,17 +79,8 @@ 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}.")
@@ -105,9 +101,27 @@ 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)
@@ -163,7 +177,7 @@ 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
 
 
@@ -178,41 +192,56 @@ def main(args, logger):
     # 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
     
-    # check blocked biomass precursors
-    cond_col_dict = adjust_biomass_precursors(logger, universe, universe, 1.0)
-    df_E = precursors_on_media(logger, universe, universe, dbexp, args.media, cond_col_dict, args.precursors)
-    if type(df_E)==int: return 1
+    if not args.justparse:
+        
+        
+        ###### CHECKS 3
+        # check growth on minmal media
+        df_G = grow_on_media(logger, universe, dbexp, args.media, '-', True)
+        if type(df_G)==int: return 1
 
-    # check blocked metabolites / dead-ends
-    df_S = biosynthesis_on_media(logger, universe, dbexp, args.media, args.biosynth)
-    if type(df_S)==int: return 1
+        # check blocked biomass precursors
+        cond_col_dict = adjust_biomass_precursors(logger, universe, universe, 1.0)
+        df_E = precursors_on_media(logger, universe, universe, dbexp, args.media, cond_col_dict, args.precursors)
+        if type(df_E)==int: return 1
+
+        # check blocked metabolites / dead-ends
+        df_S = biosynthesis_on_media(logger, universe, dbexp, args.media, args.biosynth)
+        if type(df_S)==int: return 1
 
 
     
-    ###### POLISHING 2
-    # reset growth environment befor saving the model
-    gempipe.reset_growth_env(universe)
-    
+        ###### POLISHING 2
+        # reset growth environment befor saving the model
+        gempipe.reset_growth_env(universe)
+
+        # initialize model
+        response = initialize_model(logger, universe, dbexp, args.initialize, args.media)
+        if response==1: return 1
+
+
+
+        ###### CHECKS 4
+        # compute Memote metrics
+        memote_results_dict = get_memote_results_dict(logger, universe)
+
 
 
-    # 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!")
-    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
-    sheets_dict = write_excel_model(universe, f'{args.outdir}/universe.parsedb.xlsx', args.nofigs, df_E, None, None, df_S, df_C)  
-    logger.info(f"'{args.outdir}/universe.parsedb.xlsx' created!")
+        # 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!")
+        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
+        sheets_dict = write_excel_model(universe, f'{args.outdir}/universe.parsedb.xlsx', args.nofigs, memote_results_dict, df_E, None, None, df_S, df_C)  
+        logger.info(f"'{args.outdir}/universe.parsedb.xlsx' created!")
 
 
     
-    ###### CHECKS 3
-    # check if universal escher map os updated:
+    ###### CHECKS 4
+    # check if universal escher map is updated:
     count_undrawn_rids(logger, universe, lastmap)
     
     

{gsrap-0.8.1.dist-info → gsrap-0.8.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: gsrap
-Version: 0.8.1
+Version: 0.8.3
 Summary: 
 License: GNU General Public License v3.0
 Author: Gioele Lazzari

{gsrap-0.8.1.dist-info → gsrap-0.8.3.dist-info}/RECORD

@@ -1,5 +1,5 @@
-gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=lOurIE_Gn0jYS3ks3UmX11uuMrMScHADH9ivFoLpg5k,14160
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@@ -11,67 +11,69 @@ gsrap/assets/PM4A.csv,sha256=f_5__0Ap_T0KYje5h9veW29I2qB4yU0h7Hr7WpaHjSc,9081
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@@ -91,8 +93,8 @@ gsrap/runsims/precursors.py,sha256=1RNt_Rxs0L1lolDmYh4_CiZgiwHfU5B_AcomJO6vJ28,2
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 gsrap/runsims/singleomission.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
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