gsrap 0.7.2__py3-none-any.whl → 0.8.0__py3-none-any.whl

gsrap/mkmodel/pruner.py

@@ -1,6 +1,7 @@
 import os
 import warnings
 import logging
+import pickle
 
 
 import pandas as pnd
@@ -43,22 +44,57 @@ def load_input_eggnog(logger, eggnog):
     
     
     # load eggnog annotations
-    eggnog = pnd.read_csv(eggnog, sep='\t', comment='#', header=None)
-    eggnog.columns = 'query	seed_ortholog	evalue	score	eggNOG_OGs	max_annot_lvl	COG_category	Description	Preferred_name	GOs	EC	KEGG_ko	KEGG_Pathway	KEGG_Module	KEGG_Reaction	KEGG_rclass	BRITE	KEGG_TC	CAZy	BiGG_Reaction	PFAMs'.split('\t')
-    eggnog = eggnog.set_index('query', drop=True, verify_integrity=True)
+    df_eggnog = pnd.read_csv(eggnog, sep='\t', comment='#', header=None)
+    df_eggnog.columns = 'query	seed_ortholog	evalue	score	eggNOG_OGs	max_annot_lvl	COG_category	Description	Preferred_name	GOs	EC	KEGG_ko	KEGG_Pathway	KEGG_Module	KEGG_Reaction	KEGG_rclass	BRITE	KEGG_TC	CAZy	BiGG_Reaction	PFAMs'.split('\t')
+    df_eggnog = df_eggnog.set_index('query', drop=True, verify_integrity=True)
     
     
-    return eggnog
+    return df_eggnog
 
 
 
-def parse_eggnog(eggnog):
+def load_keggorg_like_eggnog(logger, keggorg, outdir):
+    
+    
+    # load raw data, downloaded form kegg: 
+    df_keggorg = pickle.load(open(os.path.join(outdir, f'{keggorg}.keggorg'), 'rb'))
+    df_keggorg = df_keggorg.set_index('gid', drop=True, verify_integrity=True)
+
+
+    # create an eggnog-like dataframe:
+    df_eggnog_like = []   # list of dict future df
+    for gid in df_keggorg.index:
+        row_dict = {}
+
+        row_dict['query'] = gid
+        row_dict['PFAMs'] = ','.join(df_keggorg.loc[gid, 'Pfam']) if type(df_keggorg.loc[gid, 'Pfam'])==list else '-'
+        row_dict['KEGG_ko'] = df_keggorg.loc[gid, 'ko'] if type(df_keggorg.loc[gid, 'ko'])==str else '-'
+
+        df_eggnog_like.append(row_dict)
+    df_eggnog_like = pnd.DataFrame.from_records(df_eggnog_like)
+
+
+    # appen missing coluns and sort
+    eggnog_columns = 'query	seed_ortholog	evalue	score	eggNOG_OGs	max_annot_lvl	COG_category	Description	Preferred_name	GOs	EC	KEGG_ko	KEGG_Pathway	KEGG_Module	KEGG_Reaction	KEGG_rclass	BRITE	KEGG_TC	CAZy	BiGG_Reaction	PFAMs'.split('\t')
+    for c in eggnog_columns:  
+        if c not in df_eggnog_like.columns:
+            df_eggnog_like[c] = '-'
+    df_eggnog_like = df_eggnog_like[eggnog_columns]
+
+
+    # set the index like in eggnog
+    df_eggnog_like = df_eggnog_like.set_index('query', drop=True, verify_integrity=True)
+    return df_eggnog_like
+
+
+
+def parse_eggnog(df_eggnog):
     
     
     # PART 1. get KO codes available
     gid_to_kos = {}
     ko_to_gids = {}
-    for gid, kos in eggnog['KEGG_ko'].items():
+    for gid, kos in df_eggnog['KEGG_ko'].items():
         if kos == '-': 
             continue
             
@@ -229,8 +265,37 @@ def restore_gene_annotations(logger, model, universe, eggonog_gid_to_kos):
             # collect names
             names.append(uni_g.name)
         g.name = '; '.join(names)
+        
+        
+        
+def append_keggorg_gene_annots(logger, model, keggorg, outdir):
+    
 
-
+    # load raw data, downloaded form kegg: 
+    logger.info("Adding gene annotations retrieved from KEGG...")
+    df_keggorg = pickle.load(open(os.path.join(outdir, f'{keggorg}.keggorg'), 'rb'))
+    df_keggorg = df_keggorg.set_index('gid', drop=True, verify_integrity=True)
+    
+    
+    # KEGG can provide some useful (ie, used in Memote) gene annotations:
+    for g in model.genes:
+        if g.id in df_keggorg.index:
+            
+            g.annotation['kegg.genes'] = [keggorg + ':' + g.id]
+            
+            if 'NCBI-GeneID' in df_keggorg.columns:
+                g.annotation['ncbigene'] = df_keggorg.loc[g.id, 'NCBI-GeneID'] if type(df_keggorg.loc[g.id, 'NCBI-GeneID'])==list else []
+            if 'NCBI-ProteinID' in df_keggorg.columns:
+                g.annotation['ncbiprotein'] = df_keggorg.loc[g.id, 'NCBI-ProteinID'] if type(df_keggorg.loc[g.id, 'NCBI-ProteinID'])==list else []
+            if 'ASAP' in df_keggorg.columns:
+                g.annotation['asap'] = df_keggorg.loc[g.id, 'ASAP'] if type(df_keggorg.loc[g.id, 'ASAP'])==list else []
+            if 'UniProt' in df_keggorg.columns:
+                g.annotation['uniprot'] = df_keggorg.loc[g.id, 'UniProt'] if type(df_keggorg.loc[g.id, 'UniProt'])==list else []
+                
+                
+                
+            
+            
 
 
     

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

@@ -1,4 +1,6 @@
 from pathlib import Path
+import pickle
+import os
 
 
 import pandas as pnd
@@ -35,14 +37,39 @@ def parse_eggnog(model, eggnog, idcollection_dict):
     return krs_org
     
     
+
+def parse_keggorg(keggorg, outdir, idcollection_dict):
+
+    df_keggorg = pickle.load(open(os.path.join(outdir, f'{keggorg}.keggorg'), 'rb'))
+    df_keggorg = df_keggorg.set_index('gid', drop=True, verify_integrity=True)
+
+    
+    # PART 1. get KO codes available
+    kos_org = set([i for i in df_keggorg['ko'] if pnd.isna(i)==False])
+    
+    
+    # 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(): 
+        if any([ko in kos_org for ko in kos]):
+            krs_org.add(kr)
+    
+    
+    return krs_org
+
+    
     
-def check_completeness(logger, model, progress, module, focus, eggnog, idcollection_dict, summary_dict): 
+def check_completeness(logger, model, progress, module, focus, eggnog, keggorg, idcollection_dict, summary_dict, outdir): 
     # check KEGG annotations in the universe model to get '%' of completeness per pathway/module.
     
             
     # get the reference set of kr codes (all kegg or organism specific): 
     kr_uni = set()
-    if eggnog != '-':
+    if keggorg != '-':  # keggorg has precedence
+        kr_uni = parse_keggorg(keggorg, outdir, idcollection_dict)
+        kr_uni_label = f"organism code '{keggorg}'"
+    elif eggnog != '-':
         for eggfile in eggnog:
             eggset = parse_eggnog(model, eggfile, idcollection_dict)
             kr_uni = kr_uni.union(eggset)
@@ -60,7 +87,7 @@ def check_completeness(logger, model, progress, module, focus, eggnog, idcollect
                 kr_ids_modeled.add(kr_id)
     kr_uni_missing = kr_uni - kr_ids_modeled
     kr_uni_coverage = len(kr_ids_modeled.intersection(kr_uni)) / len(kr_uni) * 100
-    logger.info(f"Coverage for '{kr_uni_label}': {round(kr_uni_coverage, 0)}% ({len(kr_uni_missing)} missing).")
+    logger.info(f"Coverage for {kr_uni_label}: {round(kr_uni_coverage, 0)}% ({len(kr_uni_missing)} missing).")
     
     
     # define the map?????, containing krs not included in maps
@@ -177,15 +204,15 @@ def check_completeness(logger, model, progress, module, focus, eggnog, idcollect
         for eggfile in eggnog:
             strain = Path(eggfile).stem
             eggset = parse_eggnog(model, eggfile, idcollection_dict)
-            col = df_coverage.index.to_series().isin(eggset).astype(int)
+            col = df_coverage.index.to_series().isin(eggset).astype(int)  # integer: 0 or 1
             df_strains.append(col.rename(strain))
         df_strains = pnd.concat(df_strains, axis=1)
         # sort rows: upper rows are present in more strains
-        df_strains = df_strains.loc[df_strains.sum(axis=1).sort_values(ascending=False).index]
+        #df_strains = df_strains.loc[df_strains.sum(axis=1).sort_values(ascending=False).index]   # commented: now in charge of figures.py
         df_coverage = df_coverage.loc[df_strains.index]
         df_coverage = pnd.concat([df_coverage, df_strains], axis=1)
         # split in 2: modeled above, non-modeled below:
-        df_coverage = pnd.concat([df_coverage[df_coverage['modeled']==True], df_coverage[df_coverage['modeled']==False]])
+        #df_coverage = pnd.concat([df_coverage[df_coverage['modeled']==True], df_coverage[df_coverage['modeled']==False]])   # commented: now in charge of figures.py
     else:  # not interesting in a super-long table without strains in column
         df_coverage = None
     

gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.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
    

gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.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
@@ -72,7 +73,14 @@ 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 +161,7 @@ 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
 
 

gsrap/parsedb/completeness.py

@@ -1,4 +1,6 @@
 from pathlib import Path
+import pickle
+import os
 
 
 import pandas as pnd
@@ -35,14 +37,39 @@ def parse_eggnog(model, eggnog, idcollection_dict):
     return krs_org
     
     
+
+def parse_keggorg(keggorg, outdir, idcollection_dict):
+
+    df_keggorg = pickle.load(open(os.path.join(outdir, f'{keggorg}.keggorg'), 'rb'))
+    df_keggorg = df_keggorg.set_index('gid', drop=True, verify_integrity=True)
+
+    
+    # PART 1. get KO codes available
+    kos_org = set([i for i in df_keggorg['ko'] if pnd.isna(i)==False])
+    
+    
+    # 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(): 
+        if any([ko in kos_org for ko in kos]):
+            krs_org.add(kr)
+    
+    
+    return krs_org
+
+    
     
-def check_completeness(logger, model, progress, module, focus, eggnog, idcollection_dict, summary_dict): 
+def check_completeness(logger, model, progress, module, focus, eggnog, keggorg, idcollection_dict, summary_dict, outdir): 
     # check KEGG annotations in the universe model to get '%' of completeness per pathway/module.
     
             
     # get the reference set of kr codes (all kegg or organism specific): 
     kr_uni = set()
-    if eggnog != '-':
+    if keggorg != '-':  # keggorg has precedence
+        kr_uni = parse_keggorg(keggorg, outdir, idcollection_dict)
+        kr_uni_label = f"organism code '{keggorg}'"
+    elif eggnog != '-':
         for eggfile in eggnog:
             eggset = parse_eggnog(model, eggfile, idcollection_dict)
             kr_uni = kr_uni.union(eggset)
@@ -60,7 +87,7 @@ def check_completeness(logger, model, progress, module, focus, eggnog, idcollect
                 kr_ids_modeled.add(kr_id)
     kr_uni_missing = kr_uni - kr_ids_modeled
     kr_uni_coverage = len(kr_ids_modeled.intersection(kr_uni)) / len(kr_uni) * 100
-    logger.info(f"Coverage for '{kr_uni_label}': {round(kr_uni_coverage, 0)}% ({len(kr_uni_missing)} missing).")
+    logger.info(f"Coverage for {kr_uni_label}: {round(kr_uni_coverage, 0)}% ({len(kr_uni_missing)} missing).")
     
     
     # define the map?????, containing krs not included in maps
@@ -177,15 +204,15 @@ def check_completeness(logger, model, progress, module, focus, eggnog, idcollect
         for eggfile in eggnog:
             strain = Path(eggfile).stem
             eggset = parse_eggnog(model, eggfile, idcollection_dict)
-            col = df_coverage.index.to_series().isin(eggset).astype(int)
+            col = df_coverage.index.to_series().isin(eggset).astype(int)  # integer: 0 or 1
             df_strains.append(col.rename(strain))
         df_strains = pnd.concat(df_strains, axis=1)
         # sort rows: upper rows are present in more strains
-        df_strains = df_strains.loc[df_strains.sum(axis=1).sort_values(ascending=False).index]
+        #df_strains = df_strains.loc[df_strains.sum(axis=1).sort_values(ascending=False).index]   # commented: now in charge of figures.py
         df_coverage = df_coverage.loc[df_strains.index]
         df_coverage = pnd.concat([df_coverage, df_strains], axis=1)
         # split in 2: modeled above, non-modeled below:
-        df_coverage = pnd.concat([df_coverage[df_coverage['modeled']==True], df_coverage[df_coverage['modeled']==False]])
+        #df_coverage = pnd.concat([df_coverage[df_coverage['modeled']==True], df_coverage[df_coverage['modeled']==False]])   # commented: now in charge of figures.py
     else:  # not interesting in a super-long table without strains in column
         df_coverage = None
     

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
    

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
@@ -72,7 +73,14 @@ 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 +161,7 @@ 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
 
 

{gsrap-0.7.2.dist-info → gsrap-0.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: gsrap
-Version: 0.7.2
+Version: 0.8.0
 Summary: 
 License: GNU General Public License v3.0
 Author: Gioele Lazzari

{gsrap-0.7.2.dist-info → gsrap-0.8.0.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=JlR5ICkhkJwQrMHJOFOZg1R-0aYQAZu9h51SlC67Mtw,14064
+gsrap/__init__.py,sha256=JlR5ICkhkJwQrMHJOFOZg1R-0aYQAZu9h51SlC67Mtw,14064
 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
@@ -11,26 +11,28 @@ 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
-gsrap/commons/.ipynb_checkpoints/escherutils-checkpoint.py,sha256=lftRIKAbP4eztaZM83V3LKWZK4DtKDuCiC9A46paVoM,1148
-gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py,sha256=wQKAyWZxfy9w_uhR_DzBZz0v7vdiVM-PGDA3k1TOraI,6622
-gsrap/commons/.ipynb_checkpoints/figures-checkpoint.py,sha256=qIjyMMFrm7AkUkdYY4ZZ8SjprUfoC3brW34oHRQvNQk,3689
+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=zFTR6H7I3XeAt9_ORL0dfrwMRvshU3JPRmGif7fSY7w,7971
+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
 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
 gsrap/commons/coeffs.py,sha256=qI3_GuqHkeA2KbK9pYdkqJaFwYemAVZJGLRR4QtHt6w,19182
-gsrap/commons/downloads.py,sha256=JFrOYXrzLFhclwMtLmq8xo0QZVyjEn7QfzaTRad7y6I,8460
-gsrap/commons/escherutils.py,sha256=lftRIKAbP4eztaZM83V3LKWZK4DtKDuCiC9A46paVoM,1148
-gsrap/commons/excelhub.py,sha256=wQKAyWZxfy9w_uhR_DzBZz0v7vdiVM-PGDA3k1TOraI,6622
-gsrap/commons/figures.py,sha256=qIjyMMFrm7AkUkdYY4ZZ8SjprUfoC3brW34oHRQvNQk,3689
+gsrap/commons/downloads.py,sha256=e-7ffMD4R07MWEgXyGcwjhScbWnG7A3L100YWbpNMk0,8461
+gsrap/commons/escherutils.py,sha256=_y0TgM0-Im0RT8W8z5rr4vlnGK55iRFds6DlDsjGD-8,1151
+gsrap/commons/excelhub.py,sha256=zFTR6H7I3XeAt9_ORL0dfrwMRvshU3JPRmGif7fSY7w,7971
+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=VYKN8X1PNERP6uQDbznZXfgflLEvnw4j1T8AIAdrE7s,2902
 gsrap/commons/metrics.py,sha256=gvqF2c0e31m5qQWQ11JF4-eMqxtuONy_7lUiC7uaXX4,3291
@@ -45,29 +47,29 @@ 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=0ekGXmNULzVbkl6QW_Z8xDrHlevgtVDWEURJJR2uQRM,10323
 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=0ekGXmNULzVbkl6QW_Z8xDrHlevgtVDWEURJJR2uQRM,10323
 gsrap/mkmodel/polishing.py,sha256=R1UdFPxN8N27Iu0jsYW2N_1BkWEbBHaMYW6NkCYZK_k,3256
-gsrap/mkmodel/pruner.py,sha256=BVOK1iFXpTgZswDgAv-TgHxKB6W3iucIAo1XWrAbu4A,7009
+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=mLK2YawP9FjR3yogHhGxF2b2ti9DKmLu9uhibsq0jy4,11064
-gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py,sha256=PuIdXvkF7gmihOEMECXVZ1V4VBOld8p3lZZ2rqXjPH8,16871
+gsrap/parsedb/.ipynb_checkpoints/completeness-checkpoint.py,sha256=yhFiEslK1qmMCk_GWZ7UZtX02FUqLU39UafG5886WsY,12016
+gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py,sha256=TpW-Hp_rq6AGUQ-IVFwU8Vhij6poKWz8EF-NhdsAOsI,17414
 gsrap/parsedb/.ipynb_checkpoints/manual-checkpoint.py,sha256=F16wU8vLyM6V4F611ABuMJtwSAskL5KEgCJ7EQm_F9Y,2177
-gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=tTWohNPIrw47a08ECFTyHuT4W5KlkznllIEBCpg7Kv0,7169
+gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=OPc8PrTVD2szrmvZISlyhP1Q51AlaoQ_EghAJs4jfFU,7465
 gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py,sha256=9PgsSw-H84eN_dFUwK5FLgbqvydsdic4-VjCrZqkfnY,5703
 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
+gsrap/parsedb/completeness.py,sha256=yhFiEslK1qmMCk_GWZ7UZtX02FUqLU39UafG5886WsY,12016
+gsrap/parsedb/introduce.py,sha256=TpW-Hp_rq6AGUQ-IVFwU8Vhij6poKWz8EF-NhdsAOsI,17414
 gsrap/parsedb/manual.py,sha256=F16wU8vLyM6V4F611ABuMJtwSAskL5KEgCJ7EQm_F9Y,2177
-gsrap/parsedb/parsedb.py,sha256=tTWohNPIrw47a08ECFTyHuT4W5KlkznllIEBCpg7Kv0,7169
+gsrap/parsedb/parsedb.py,sha256=OPc8PrTVD2szrmvZISlyhP1Q51AlaoQ_EghAJs4jfFU,7465
 gsrap/parsedb/repeating.py,sha256=9PgsSw-H84eN_dFUwK5FLgbqvydsdic4-VjCrZqkfnY,5703
 gsrap/runsims/.ipynb_checkpoints/__init__-checkpoint.py,sha256=6E6E1gWgH0V7ls4Omx4mxxC85gMJ_27YqhjugJzlZtY,97
 gsrap/runsims/.ipynb_checkpoints/biosynth-checkpoint.py,sha256=fUlHUo4CfB4rGX9Dth87B1p5E5sz7i6spR7ZoqDDGaI,2836
@@ -87,8 +89,8 @@ 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-0.7.2.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gsrap-0.7.2.dist-info/METADATA,sha256=bZQ9_fiR3Fo5_mUcnWD4GgMRYtFDjO0LG74yxtjSkBs,898
-gsrap-0.7.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-gsrap-0.7.2.dist-info/entry_points.txt,sha256=S9MY0DjfnbKGlZbp5bV7W6dNFy3APoEV84u9x6MV1eI,36
-gsrap-0.7.2.dist-info/RECORD,,
+gsrap-0.8.0.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
+gsrap-0.8.0.dist-info/METADATA,sha256=T5COI9B29df6TdmUbZvFrQsficCTN3SVzJGHJ5yw4Us,898
+gsrap-0.8.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
+gsrap-0.8.0.dist-info/entry_points.txt,sha256=S9MY0DjfnbKGlZbp5bV7W6dNFy3APoEV84u9x6MV1eI,36
+gsrap-0.8.0.dist-info/RECORD,,