gsrap 0.7.1__py3-none-any.whl → 0.8.0__py3-none-any.whl

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
@@ -153,9 +161,8 @@ def main(args, logger):
     
     ###### CHECKS 1
     # check universe completness
-    setattr(args, 'zeroes', True)  # old parameter, forced to True from v0.6.1
-    response = check_completeness(logger, universe, args.progress, args.module, args.focus, args.eggnog, args.zeroes, idcollection_dict, summary_dict)
-    if response==1: return 1
+    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
 
 
 
@@ -194,7 +201,7 @@ def main(args, logger):
     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', df_E, None, None, df_S)  
+    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!")
 
 

gsrap/parsedb/completeness.py

@@ -1,3 +1,8 @@
+from pathlib import Path
+import pickle
+import os
+
+
 import pandas as pnd
 
 
@@ -32,14 +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)
     
-def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, idcollection_dict, summary_dict): 
+    
+    return krs_org
+
+    
+    
+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)
@@ -55,10 +85,22 @@ def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, i
         if 'kegg.reaction' in r.annotation.keys():
             for kr_id in r.annotation['kegg.reaction']:
                 kr_ids_modeled.add(kr_id)
-    kr_uni_missing = len(kr_uni - kr_ids_modeled.intersection(kr_uni))
+    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)}% ({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
+    krs_in_maps = set()
+    for i in summary_dict: krs_in_maps = krs_in_maps.union(i['kr_ids']) 
+    krs_not_in_maps = idcollection_dict['kr'] - krs_in_maps
+    summary_dict.append({
+        'map_id': 'map?????',
+        'map_name': 'Not included in maps',
+        'kr_ids': krs_not_in_maps,
+        'cnt_r': len(krs_not_in_maps),
+        'mds': []
+    })    
     
     
     # get all the map / md codes:
@@ -112,52 +154,77 @@ def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, i
             missing_logger = (map_id, missing)
 
         
+        # put the map in the right bucket:
         if missing == set() and map_krs != set():
             maps_finished.add(map_id)
-            
         elif map_krs == set():
             maps_noreac.add(map_id)
-            
         elif missing == map_krs:
             maps_missing.add(map_id)
-            
-            if zeroes:
-                list_coverage.append({
-                    'map_id': map_id,
-                    'map_name_short': map_name_short, 
-                    'perc_completeness': 0,
-                    'perc_completeness_str': ' 0',
-                    'present': present,
-                    'missing': missing,
-                    'md_ids': [j['md_id'] for j in i['mds']],
-                })
-            
         elif len(missing) < len(map_krs):
             maps_partial.add(map_id)
             
-            # get '%' of completeness:
-            perc_completeness = len(present)/len(map_krs)*100
-            perc_completeness_str = str(round(perc_completeness))   # version to be printed
-            if len(perc_completeness_str)==1: 
-                perc_completeness_str = ' ' + perc_completeness_str
-                
-            list_coverage.append({
-                'map_id': map_id,
-                'map_name_short': map_name_short, 
-                'perc_completeness': perc_completeness,
-                'perc_completeness_str': perc_completeness_str,
-                'present': present,
-                'missing': missing,
-                'md_ids': [j['md_id'] for j in i['mds']],
-            })
             
+        # get '%' of completeness:
+        if len(map_krs) != 0: perc_completeness = len(present)/len(map_krs)*100
+        else: perc_completeness = 100   # for maps_noreac
+        perc_completeness_str = str(round(perc_completeness))   # version to be printed
+        if len(perc_completeness_str)==1: 
+            perc_completeness_str = ' ' + perc_completeness_str
+
             
-    # order list by '%' of completness and print:
+        # append map to list:
+        list_coverage.append({
+            'map_id': map_id,
+            'map_name_short': map_name_short, 
+            'perc_completeness': perc_completeness,
+            'perc_completeness_str': perc_completeness_str,
+            'present': present,
+            'missing': missing,
+            'md_ids': [j['md_id'] for j in i['mds']],
+        })
+        
+        
+    
+    # create coverage dataframe
+    if eggnog != '-' and len(eggnog) >= 2:  
+        df_coverage = {}
+        for i in list_coverage:
+            for kr in i['present'].union(i['missing']):
+                if kr not in df_coverage.keys(): 
+                    df_coverage[kr] = {'map_ids': set()}
+                df_coverage[kr]['map_ids'].add(i['map_id'])
+        df_coverage = pnd.DataFrame.from_records(df_coverage).T
+        df_coverage['modeled'] = False
+        for kr, row in df_coverage.iterrows():
+            if kr in kr_ids_modeled:
+                df_coverage.loc[kr, 'modeled'] = True
+        # build strain columns all at once
+        df_strains = []  # list of small DataFrames
+        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)  # 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]   # 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]])   # commented: now in charge of figures.py
+    else:  # not interesting in a super-long table without strains in column
+        df_coverage = None
+    
+           
+            
+    # order list by '%' of completness and print if needed:
     list_coverage = sorted(list_coverage, key=lambda x: x['perc_completeness'], reverse=True)
     for i in list_coverage:
         if progress:
             if focus=='-' or focus in i['md_ids'] or focus==i['map_id']:
-                logger.info(f"{i['map_id']}: {i['map_name_short']} {i['perc_completeness_str']}% completed, {len(i['present'])} added, {len(i['missing'])} missing.")
+                if i['map_id'] in maps_missing or i['map_id'] in maps_partial:
+                    logger.info(f"{i['map_id']}: {i['map_name_short']} {i['perc_completeness_str']}% completed, {len(i['present'])} added, {len(i['missing'])} missing.")
         
         
         # get the correspondent pathway element of the 'summary_dict'
@@ -199,50 +266,43 @@ def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, i
                 missing_logger = (md_id, missing)
             
             
+            # put the map in the right bucket:
             if missing == set() and md_krs != set():
                 mds_completed.add(md_id)
-
             elif md_krs == set():
                 mds_noreac.add(md_id)
-
             elif missing == md_krs:
                 mds_missing.add(md_id)
-                
-                if zeroes:
-                    list_coverage_md.append({
-                        'md_id': md_id,
-                        'md_name_short': md_name_short, 
-                        'perc_completeness': 0,
-                        'perc_completeness_str': ' 0',
-                        'present': present,
-                        'missing': missing,
-                    })
-                
             elif len(missing) < len(md_krs):
                 mds_partial.add(md_id)
 
-                # get '%' of completeness:
-                perc_completeness = len(present)/len(md_krs)*100
-                perc_completeness_str = str(round(perc_completeness))   # version to be printed
-                if len(perc_completeness_str)==1: 
-                    perc_completeness_str = ' ' + perc_completeness_str
+                
+            # get '%' of completeness:
+            if len(md_krs) != 0: perc_completeness = len(present)/len(md_krs)*100
+            else: perc_completeness = 100   # for mds_noreac
+            perc_completeness_str = str(round(perc_completeness))   # version to be printed
+            if len(perc_completeness_str)==1: 
+                perc_completeness_str = ' ' + perc_completeness_str
 
-                list_coverage_md.append({
-                    'md_id': md_id,
-                    'md_name_short': md_name_short, 
-                    'perc_completeness': perc_completeness,
-                    'perc_completeness_str': perc_completeness_str,
-                    'present': present,
-                    'missing': missing,
-                })
+                
+            # append md to list:
+            list_coverage_md.append({
+                'md_id': md_id,
+                'md_name_short': md_name_short, 
+                'perc_completeness': perc_completeness,
+                'perc_completeness_str': perc_completeness_str,
+                'present': present,
+                'missing': missing,
+            })
                
             
-        # order list by '%' of completness and print:
+        # order list by '%' of completness and print if needed:
         list_coverage_md = sorted(list_coverage_md, key=lambda x: x['perc_completeness'], reverse=True)
         for z in list_coverage_md:
             if module:
                 if focus=='-' or focus==z['md_id']:
-                    logger.info(f"{spacer}{z['md_id']}: {z['md_name_short']} {z['perc_completeness_str']}% completed, {len(z['present'])} added, {len(z['missing'])} missing.")
+                    if z['md_id'] in mds_missing or z['md_id'] in mds_partial:
+                        logger.info(f"{spacer}{z['md_id']}: {z['md_name_short']} {z['perc_completeness_str']}% completed, {len(z['present'])} added, {len(z['missing'])} missing.")
         
         
         # print summary:
@@ -254,6 +314,6 @@ def check_completeness(logger, model, progress, module, focus, eggnog, zeroes, i
         logger.info(f"Maps: finished {len(maps_finished)} - partial {len(maps_partial)} - missing {len(maps_missing)} - noreac {len(maps_noreac)}")
             
         
-    return 0     
+    return df_coverage     
 
 

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
@@ -153,9 +161,8 @@ def main(args, logger):
     
     ###### CHECKS 1
     # check universe completness
-    setattr(args, 'zeroes', True)  # old parameter, forced to True from v0.6.1
-    response = check_completeness(logger, universe, args.progress, args.module, args.focus, args.eggnog, args.zeroes, idcollection_dict, summary_dict)
-    if response==1: return 1
+    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
 
 
 
@@ -194,7 +201,7 @@ def main(args, logger):
     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', df_E, None, None, df_S)  
+    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!")
 
 

gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py

@@ -57,9 +57,9 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
         df_G.loc[obj_id, f'{medium}'] = res_fba
         if universe_in_parsedb:
             if res_fba == 'infeasible' or res_fba == 0.0:
-                logger.warning(f"Growth on '{medium}': {res_fba}.")
+                logger.warning(f"Growth on medium '{medium}': {res_fba}.")
             else:
-                logger.info(f"Growth on '{medium}': {res_fba}.")
+                logger.info(f"Growth on medium '{medium}': {res_fba}.")
         
         
         # perform FVA if requested:

gsrap/runsims/simplegrowth.py

@@ -57,9 +57,9 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
         df_G.loc[obj_id, f'{medium}'] = res_fba
         if universe_in_parsedb:
             if res_fba == 'infeasible' or res_fba == 0.0:
-                logger.warning(f"Growth on '{medium}': {res_fba}.")
+                logger.warning(f"Growth on medium '{medium}': {res_fba}.")
             else:
-                logger.info(f"Growth on '{medium}': {res_fba}.")
+                logger.info(f"Growth on medium '{medium}': {res_fba}.")
         
         
         # perform FVA if requested:

{gsrap-0.7.1.dist-info → gsrap-0.8.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: gsrap
-Version: 0.7.1
+Version: 0.8.0
 Summary: 
 License: GNU General Public License v3.0
 Author: Gioele Lazzari
@@ -17,9 +17,11 @@ Requires-Dist: cobra (>=0.29)
 Requires-Dist: colorlog (>=6.9.0)
 Requires-Dist: gdown (>=5.2.0)
 Requires-Dist: gempipe (>=1.38.1)
+Requires-Dist: matplotlib (>=3.9.0)
 Requires-Dist: memote (>=0.17.0)
 Requires-Dist: openpyxl (>=3.1.0)
 Requires-Dist: pandas (>=2.0.0)
+Requires-Dist: xlsxwriter (>=3.1.0)
 Description-Content-Type: text/markdown
 
 Source code for `gsrap`.

{gsrap-0.7.1.dist-info → gsrap-0.8.0.dist-info}/RECORD

@@ -1,5 +1,5 @@
-gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=93coHbPQfWL7XSudRvKh5RGgqJbyOvECVmMaHPfShOU,13693
-gsrap/__init__.py,sha256=93coHbPQfWL7XSudRvKh5RGgqJbyOvECVmMaHPfShOU,13693
+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
@@ -11,24 +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=XO7ZZFqORB1nnH1Nj07VSGr18em1rt_AH6oAqwqhp4o,5867
+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=XO7ZZFqORB1nnH1Nj07VSGr18em1rt_AH6oAqwqhp4o,5867
+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
@@ -43,29 +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=bXKBU8sUhRWKU-MYqiHgZFEwqvpAtoJa6_1h6D94REM,8537
+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=bXKBU8sUhRWKU-MYqiHgZFEwqvpAtoJa6_1h6D94REM,8537
+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=5P_OxGfKXSJDDV0qIcd6xQvAJymsMQKvhsUvMl79dkk,9478
-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=F0vYUvlFkBvg1Jis1nNJ9cS4f3tSF61hbM4zg7D3OJs,7242
+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=5P_OxGfKXSJDDV0qIcd6xQvAJymsMQKvhsUvMl79dkk,9478
-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=F0vYUvlFkBvg1Jis1nNJ9cS4f3tSF61hbM4zg7D3OJs,7242
+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
@@ -74,7 +78,7 @@ gsrap/runsims/.ipynb_checkpoints/essentialgenes-checkpoint.py,sha256=MzHiuaU1gwi
 gsrap/runsims/.ipynb_checkpoints/growthfactors-checkpoint.py,sha256=r_W4idtOSJBDh7HURRsU8s1TqfOZ3TfeVw2HHDxmnGU,2265
 gsrap/runsims/.ipynb_checkpoints/precursors-checkpoint.py,sha256=1RNt_Rxs0L1lolDmYh4_CiZgiwHfU5B_AcomJO6vJ28,2219
 gsrap/runsims/.ipynb_checkpoints/runsims-checkpoint.py,sha256=2FC5Gs8oSYyZTjHF3A7aXB_O6myVfcn3bCxQfLJlZTk,2842
-gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py,sha256=whNezVUgdTFO5H8_Q6_jo5rM-zyzj17bzGDcrxfTotc,2339
+gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py,sha256=tCQHTMUqum1YwlBKRTNaQoag2co_yQlCaKmISOARAlE,2353
 gsrap/runsims/.ipynb_checkpoints/singleomission-checkpoint.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
 gsrap/runsims/__init__.py,sha256=6E6E1gWgH0V7ls4Omx4mxxC85gMJ_27YqhjugJzlZtY,97
 gsrap/runsims/biosynth.py,sha256=fUlHUo4CfB4rGX9Dth87B1p5E5sz7i6spR7ZoqDDGaI,2836
@@ -83,10 +87,10 @@ gsrap/runsims/essentialgenes.py,sha256=MzHiuaU1gwiPdjZAgG7tkdYzkTTvoNCLp5tkezZhz
 gsrap/runsims/growthfactors.py,sha256=r_W4idtOSJBDh7HURRsU8s1TqfOZ3TfeVw2HHDxmnGU,2265
 gsrap/runsims/precursors.py,sha256=1RNt_Rxs0L1lolDmYh4_CiZgiwHfU5B_AcomJO6vJ28,2219
 gsrap/runsims/runsims.py,sha256=2FC5Gs8oSYyZTjHF3A7aXB_O6myVfcn3bCxQfLJlZTk,2842
-gsrap/runsims/simplegrowth.py,sha256=whNezVUgdTFO5H8_Q6_jo5rM-zyzj17bzGDcrxfTotc,2339
+gsrap/runsims/simplegrowth.py,sha256=tCQHTMUqum1YwlBKRTNaQoag2co_yQlCaKmISOARAlE,2353
 gsrap/runsims/singleomission.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
-gsrap-0.7.1.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
-gsrap-0.7.1.dist-info/METADATA,sha256=ps1z-ZR33q-YL1KeATh-RUNNuB4VU47Mz4OAl2b1F24,826
-gsrap-0.7.1.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
-gsrap-0.7.1.dist-info/entry_points.txt,sha256=S9MY0DjfnbKGlZbp5bV7W6dNFy3APoEV84u9x6MV1eI,36
-gsrap-0.7.1.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,,