gsrap 0.7.0__py3-none-any.whl → 0.7.2__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (33) hide show
  1. gsrap/.ipynb_checkpoints/__init__-checkpoint.py +34 -5
  2. gsrap/__init__.py +34 -5
  3. gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py +4 -0
  4. gsrap/commons/.ipynb_checkpoints/coeffs-checkpoint.py +1 -1
  5. gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py +27 -3
  6. gsrap/commons/.ipynb_checkpoints/figures-checkpoint.py +105 -0
  7. gsrap/commons/.ipynb_checkpoints/fluxbal-checkpoint.py +1 -1
  8. gsrap/commons/biomass.py +4 -0
  9. gsrap/commons/coeffs.py +1 -1
  10. gsrap/commons/excelhub.py +27 -3
  11. gsrap/commons/figures.py +105 -0
  12. gsrap/commons/fluxbal.py +1 -1
  13. gsrap/mkmodel/.ipynb_checkpoints/gapfillutils-checkpoint.py +3 -0
  14. gsrap/mkmodel/.ipynb_checkpoints/mkmodel-checkpoint.py +11 -4
  15. gsrap/mkmodel/gapfillutils.py +3 -0
  16. gsrap/mkmodel/mkmodel.py +11 -4
  17. gsrap/parsedb/.ipynb_checkpoints/annotation-checkpoint.py +3 -0
  18. gsrap/parsedb/.ipynb_checkpoints/completeness-checkpoint.py +101 -65
  19. gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py +16 -1
  20. gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py +4 -5
  21. gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py +7 -0
  22. gsrap/parsedb/annotation.py +3 -0
  23. gsrap/parsedb/completeness.py +101 -65
  24. gsrap/parsedb/introduce.py +16 -1
  25. gsrap/parsedb/parsedb.py +4 -5
  26. gsrap/parsedb/repeating.py +7 -0
  27. gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py +6 -7
  28. gsrap/runsims/simplegrowth.py +6 -7
  29. {gsrap-0.7.0.dist-info → gsrap-0.7.2.dist-info}/METADATA +3 -1
  30. {gsrap-0.7.0.dist-info → gsrap-0.7.2.dist-info}/RECORD +33 -31
  31. {gsrap-0.7.0.dist-info → gsrap-0.7.2.dist-info}/LICENSE.txt +0 -0
  32. {gsrap-0.7.0.dist-info → gsrap-0.7.2.dist-info}/WHEEL +0 -0
  33. {gsrap-0.7.0.dist-info → gsrap-0.7.2.dist-info}/entry_points.txt +0 -0
gsrap/parsedb/introduce.py CHANGED
@@ -141,6 +141,10 @@ def introduce_metabolites(logger, db, model, idcollection_dict, kegg_compound_to
141
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  # save as list:
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  for ankey in ankeys:
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  m.annotation[ankey] = list(m.annotation[ankey])
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+
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+
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+ # add SBO annotation
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+ m.annotation['sbo'] = ['SBO:0000247'] # generic metabolite
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145
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@@ -264,7 +268,8 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
264
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  m_e.name = m_c.name
265
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  m_e.formula = m_c.formula
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  m_e.charge = m_c.charge
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- m_e.annotation = m_c.annotation
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+
272
+ m_e.annotation = m_c.annotation # transfer all annotations, including SBO!
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273
 
269
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  def add_exchange_reaction(model, mid_e):
@@ -283,6 +288,10 @@ def introduce_transporters(logger, db, model, idcollection_dict, kegg_reaction_t
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  r.bounds = (-1000, 1000)
284
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  else:
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  r.bounds = (0, 1000)
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+
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+ # add SBO annotation
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+ r.annotation['sbo'] = ['SBO:0000627'] # exchange reaction
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+
286
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287
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@@ -418,6 +427,9 @@ def introduce_sinks_demands(logger, model):
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  r.name = f"Sink for {model.metabolites.get_by_id(f'{puremid}_c').name}"
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  r.build_reaction_from_string(f'{puremid}_c <=> ')
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  r.bounds = (-1000, 1000)
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+
431
+ # add SBO annotation
432
+ r.annotation['sbo'] = ['SBO:0000632'] # sink reaction
421
433
 
422
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  for puremid in demands:
@@ -427,6 +439,9 @@ def introduce_sinks_demands(logger, model):
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  r.name = f"Demand for {model.metabolites.get_by_id(f'{puremid}_c').name}"
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  r.build_reaction_from_string(f'{puremid}_c --> ')
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  r.bounds = (0, 1000)
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+
443
+ # add SBO annotation
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+ r.annotation['sbo'] = ['SBO:0000628'] # demand reaction
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445
 
431
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  return model
gsrap/parsedb/parsedb.py CHANGED
@@ -113,7 +113,7 @@ def main(args, logger):
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  ###### RECONSTRUCTION
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  # create the model
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- universe = cobra.Model('newuni')
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+ universe = cobra.Model('universe')
117
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  logger.info("Parsing gsrap database...")
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118
 
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  # introduce M / R / T
@@ -153,9 +153,8 @@ def main(args, logger):
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  ###### CHECKS 1
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  # check universe completness
156
- setattr(args, 'zeroes', True) # old parameter, forced to True from v0.6.1
157
- response = check_completeness(logger, universe, args.progress, args.module, args.focus, args.eggnog, args.zeroes, idcollection_dict, summary_dict)
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- if response==1: return 1
156
+ df_C = check_completeness(logger, universe, args.progress, args.module, args.focus, args.eggnog, idcollection_dict, summary_dict)
157
+ if type(df_C)==int: return 1
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@@ -194,7 +193,7 @@ def main(args, logger):
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  cobra.io.write_sbml_model(universe, f'{args.outdir}/universe.xml') # groups are saved only to SBML
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  logger.info(f"'{args.outdir}/universe.xml' created!")
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  force_id_on_sbml(f'{args.outdir}/universe.xml', 'universe') # force introduction of the 'id=""' field
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- sheets_dict = write_excel_model(universe, f'{args.outdir}/universe.parsedb.xlsx', df_E, None, None, df_S)
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+ sheets_dict = write_excel_model(universe, f'{args.outdir}/universe.parsedb.xlsx', args.nofigs, df_E, None, None, df_S, df_C)
198
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  logger.info(f"'{args.outdir}/universe.parsedb.xlsx' created!")
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gsrap/parsedb/repeating.py CHANGED
@@ -125,6 +125,13 @@ def add_reaction(logger, model, rid, row, kr_ids, kegg_reaction_to_others, addty
125
125
  r.annotation[ankey] = list(r.annotation[ankey])
126
126
 
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128
+ # add SBO annotation
129
+ if addtype=='R':
130
+ r.annotation['sbo'] = ['SBO:0000176'] # metabolic reaction
131
+ else:
132
+ r.annotation['sbo'] = ['SBO:0000185'] # transport reaction
133
+
134
+
128
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  # check if unbalanced
129
136
  if r.check_mass_balance() != {}:
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  logger.error(f"{itemtype} '{r.id}' is unbalanced: {r.check_mass_balance()}.")
gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py CHANGED
@@ -12,9 +12,7 @@ from ..commons import verify_growth
12
12
  def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
13
13
 
14
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- # if working with the universe:
16
- if universe_in_parsedb:
17
- log_for_parsedb = []
15
+
18
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  # check if requested
@@ -58,7 +56,10 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
58
56
  res_fba = verify_growth(model, boolean=False)
59
57
  df_G.loc[obj_id, f'{medium}'] = res_fba
60
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  if universe_in_parsedb:
61
- log_for_parsedb.append(f"'{medium}': {res_fba}")
59
+ if res_fba == 'infeasible' or res_fba == 0.0:
60
+ logger.warning(f"Growth on medium '{medium}': {res_fba}.")
61
+ else:
62
+ logger.info(f"Growth on medium '{medium}': {res_fba}.")
62
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63
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64
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  # perform FVA if requested:
@@ -68,7 +69,5 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
68
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  for rid, row in df_fva.iterrows():
69
70
  df_G.loc[rid, f'{medium}'] = f"({round(row['minimum'], 3)}, {round(row['maximum'], 3)})"
70
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71
-
72
- if universe_in_parsedb:
73
- logger.info(f"Results: {'; '.join(log_for_parsedb)}.")
72
+
74
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  return df_G
gsrap/runsims/simplegrowth.py CHANGED
@@ -12,9 +12,7 @@ from ..commons import verify_growth
12
12
  def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
13
13
 
14
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15
- # if working with the universe:
16
- if universe_in_parsedb:
17
- log_for_parsedb = []
15
+
18
16
 
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20
18
  # check if requested
@@ -58,7 +56,10 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
58
56
  res_fba = verify_growth(model, boolean=False)
59
57
  df_G.loc[obj_id, f'{medium}'] = res_fba
60
58
  if universe_in_parsedb:
61
- log_for_parsedb.append(f"'{medium}': {res_fba}")
59
+ if res_fba == 'infeasible' or res_fba == 0.0:
60
+ logger.warning(f"Growth on medium '{medium}': {res_fba}.")
61
+ else:
62
+ logger.info(f"Growth on medium '{medium}': {res_fba}.")
62
63
 
63
64
 
64
65
  # perform FVA if requested:
@@ -68,7 +69,5 @@ def grow_on_media(logger, model, dbexp, media, fva, universe_in_parsedb=False):
68
69
  for rid, row in df_fva.iterrows():
69
70
  df_G.loc[rid, f'{medium}'] = f"({round(row['minimum'], 3)}, {round(row['maximum'], 3)})"
70
71
 
71
-
72
- if universe_in_parsedb:
73
- logger.info(f"Results: {'; '.join(log_for_parsedb)}.")
72
+
74
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  return df_G
{gsrap-0.7.0.dist-info → gsrap-0.7.2.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.3
2
2
  Name: gsrap
3
- Version: 0.7.0
3
+ Version: 0.7.2
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  Summary:
5
5
  License: GNU General Public License v3.0
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  Author: Gioele Lazzari
@@ -17,9 +17,11 @@ Requires-Dist: cobra (>=0.29)
17
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  Requires-Dist: colorlog (>=6.9.0)
18
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  Requires-Dist: gdown (>=5.2.0)
19
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  Requires-Dist: gempipe (>=1.38.1)
20
+ Requires-Dist: matplotlib (>=3.9.0)
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  Requires-Dist: memote (>=0.17.0)
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  Requires-Dist: openpyxl (>=3.1.0)
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  Requires-Dist: pandas (>=2.0.0)
24
+ Requires-Dist: xlsxwriter (>=3.1.0)
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  Description-Content-Type: text/markdown
24
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  Source code for `gsrap`.
{gsrap-0.7.0.dist-info → gsrap-0.7.2.dist-info}/RECORD RENAMED
@@ -1,5 +1,5 @@
1
- gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=OKMs5wy3RsxLLsD-fOfF0MCVKaxUOtlemcGa3ywyKWI,12390
2
- gsrap/__init__.py,sha256=OKMs5wy3RsxLLsD-fOfF0MCVKaxUOtlemcGa3ywyKWI,12390
1
+ gsrap/.ipynb_checkpoints/__init__-checkpoint.py,sha256=nTCojQmYOSv1tRDBEZu7p2Ne_jB9xTUEIylln19tHkk,13818
2
+ gsrap/__init__.py,sha256=nTCojQmYOSv1tRDBEZu7p2Ne_jB9xTUEIylln19tHkk,13818
3
3
  gsrap/assets/.ipynb_checkpoints/PM1-checkpoint.csv,sha256=0qjaMVG_t9aFxbHbxON6ecmEUnWPwN9nhmxc61QFeCU,8761
4
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  gsrap/assets/.ipynb_checkpoints/PM2A-checkpoint.csv,sha256=rjYTdwe8lpRS552BYiUP3J71juG2ywVdR5Sux6fjZTY,8816
5
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  gsrap/assets/.ipynb_checkpoints/PM3B-checkpoint.csv,sha256=42IGX_2O5bRYSiHoMuVKT-T-bzVj0cSRZBvGOrbnQMA,8130
@@ -12,23 +12,25 @@ gsrap/assets/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
12
12
  gsrap/assets/kegg_compound_to_others.pickle,sha256=pz1897cfQ7PLsYZiBVcoMQPzvRzT-nHUdgphBe0g5ZQ,8233860
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  gsrap/assets/kegg_reaction_to_others.pickle,sha256=AGW8CGN5hKeXZoYn3JRF4Xu832WyNrTlMcLw7luttlc,1703146
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  gsrap/commons/.ipynb_checkpoints/__init__-checkpoint.py,sha256=P_rdjFcL_FjkKYT3a0IJiQTzWL7p2Hm6z-hjuCZEHgU,216
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- gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py,sha256=P5jjB-oIgHyYEqPIKsC_Ik1xhiiJzi_piVd-zPaBzg4,17889
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- gsrap/commons/.ipynb_checkpoints/coeffs-checkpoint.py,sha256=wDh7VhTQrFpRKe2ijbnBU6cXjoeEvJxed6eNEBx-8Yc,19186
15
+ gsrap/commons/.ipynb_checkpoints/biomass-checkpoint.py,sha256=4u7WBaUgo42tBoXDU1D0VUjICatb44e0jfswZrBeHYs,17987
16
+ gsrap/commons/.ipynb_checkpoints/coeffs-checkpoint.py,sha256=qI3_GuqHkeA2KbK9pYdkqJaFwYemAVZJGLRR4QtHt6w,19182
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  gsrap/commons/.ipynb_checkpoints/downloads-checkpoint.py,sha256=JFrOYXrzLFhclwMtLmq8xo0QZVyjEn7QfzaTRad7y6I,8460
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18
  gsrap/commons/.ipynb_checkpoints/escherutils-checkpoint.py,sha256=lftRIKAbP4eztaZM83V3LKWZK4DtKDuCiC9A46paVoM,1148
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- gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py,sha256=XO7ZZFqORB1nnH1Nj07VSGr18em1rt_AH6oAqwqhp4o,5867
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- gsrap/commons/.ipynb_checkpoints/fluxbal-checkpoint.py,sha256=ZXbC6DjW5mAPaF5POh98mQHDWl9a7t9q6GFx9IlVs9g,1260
19
+ gsrap/commons/.ipynb_checkpoints/excelhub-checkpoint.py,sha256=wQKAyWZxfy9w_uhR_DzBZz0v7vdiVM-PGDA3k1TOraI,6622
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+ gsrap/commons/.ipynb_checkpoints/figures-checkpoint.py,sha256=qIjyMMFrm7AkUkdYY4ZZ8SjprUfoC3brW34oHRQvNQk,3689
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+ gsrap/commons/.ipynb_checkpoints/fluxbal-checkpoint.py,sha256=jgC3-vI9Tbjvqohh2mJwFra4rl_pbUzHWrSa_QAxVO4,1262
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  gsrap/commons/.ipynb_checkpoints/logutils-checkpoint.py,sha256=VsnrkIsUftS3MOOwAd0n0peQ7a2X5ZEx930eCtzmW7g,1317
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  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
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  gsrap/commons/.ipynb_checkpoints/sbmlutils-checkpoint.py,sha256=gkY02qbGXrbYStn2F8J0KM0fmqati2Nbvi128EF7coI,365
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  gsrap/commons/__init__.py,sha256=P_rdjFcL_FjkKYT3a0IJiQTzWL7p2Hm6z-hjuCZEHgU,216
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- gsrap/commons/biomass.py,sha256=P5jjB-oIgHyYEqPIKsC_Ik1xhiiJzi_piVd-zPaBzg4,17889
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- gsrap/commons/coeffs.py,sha256=wDh7VhTQrFpRKe2ijbnBU6cXjoeEvJxed6eNEBx-8Yc,19186
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+ gsrap/commons/biomass.py,sha256=4u7WBaUgo42tBoXDU1D0VUjICatb44e0jfswZrBeHYs,17987
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+ gsrap/commons/coeffs.py,sha256=qI3_GuqHkeA2KbK9pYdkqJaFwYemAVZJGLRR4QtHt6w,19182
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  gsrap/commons/downloads.py,sha256=JFrOYXrzLFhclwMtLmq8xo0QZVyjEn7QfzaTRad7y6I,8460
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  gsrap/commons/escherutils.py,sha256=lftRIKAbP4eztaZM83V3LKWZK4DtKDuCiC9A46paVoM,1148
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- gsrap/commons/excelhub.py,sha256=XO7ZZFqORB1nnH1Nj07VSGr18em1rt_AH6oAqwqhp4o,5867
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- gsrap/commons/fluxbal.py,sha256=ZXbC6DjW5mAPaF5POh98mQHDWl9a7t9q6GFx9IlVs9g,1260
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+ gsrap/commons/excelhub.py,sha256=wQKAyWZxfy9w_uhR_DzBZz0v7vdiVM-PGDA3k1TOraI,6622
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+ gsrap/commons/figures.py,sha256=qIjyMMFrm7AkUkdYY4ZZ8SjprUfoC3brW34oHRQvNQk,3689
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+ gsrap/commons/fluxbal.py,sha256=jgC3-vI9Tbjvqohh2mJwFra4rl_pbUzHWrSa_QAxVO4,1262
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  gsrap/commons/logutils.py,sha256=VsnrkIsUftS3MOOwAd0n0peQ7a2X5ZEx930eCtzmW7g,1317
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  gsrap/commons/medium.py,sha256=VYKN8X1PNERP6uQDbznZXfgflLEvnw4j1T8AIAdrE7s,2902
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  gsrap/commons/metrics.py,sha256=gvqF2c0e31m5qQWQ11JF4-eMqxtuONy_7lUiC7uaXX4,3291
@@ -42,31 +44,31 @@ gsrap/getmaps/kdown.py,sha256=mv5wqP4DX9KhB1IIWx6cLrc-MjQdF5Nz-Gii8QSO_6I,24498
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  gsrap/mkmodel/.ipynb_checkpoints/__init__-checkpoint.py,sha256=PNze-26HMOwfdJ92KiXpr--VV1ftVfo3CAxBZgeokp8,92
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  gsrap/mkmodel/.ipynb_checkpoints/biologcuration-checkpoint.py,sha256=Nn7z-js-mzzeO23kVM2L7sJ5PNle7AkCUeBcEAYjlFU,15378
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  gsrap/mkmodel/.ipynb_checkpoints/gapfill-checkpoint.py,sha256=BPZw4sszlBhAYfHnV0pA7EpG0b2ePwS6kUfFt0Ww-ss,5159
45
- gsrap/mkmodel/.ipynb_checkpoints/gapfillutils-checkpoint.py,sha256=XEuiX_38HBDYWOM6wVSY6UI9nuqbo9pzLOhERSt1P-g,3063
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- gsrap/mkmodel/.ipynb_checkpoints/mkmodel-checkpoint.py,sha256=cS8h5TTPjqzaw9jlIbb-MUfEFkHHEo59oEHItID_hvc,8506
47
+ gsrap/mkmodel/.ipynb_checkpoints/gapfillutils-checkpoint.py,sha256=S6nFUZ1Bbdf13nVJhGK2S5C_V3hd5zwTg2o5nzejngg,3123
48
+ gsrap/mkmodel/.ipynb_checkpoints/mkmodel-checkpoint.py,sha256=5dW5eAKW9iAFlPITM-0ZjL2FmFp3OTSvLI-xbJ-zGgs,8550
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  gsrap/mkmodel/.ipynb_checkpoints/polishing-checkpoint.py,sha256=R1UdFPxN8N27Iu0jsYW2N_1BkWEbBHaMYW6NkCYZK_k,3256
48
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  gsrap/mkmodel/.ipynb_checkpoints/pruner-checkpoint.py,sha256=BVOK1iFXpTgZswDgAv-TgHxKB6W3iucIAo1XWrAbu4A,7009
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  gsrap/mkmodel/__init__.py,sha256=PNze-26HMOwfdJ92KiXpr--VV1ftVfo3CAxBZgeokp8,92
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  gsrap/mkmodel/biologcuration.py,sha256=Nn7z-js-mzzeO23kVM2L7sJ5PNle7AkCUeBcEAYjlFU,15378
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  gsrap/mkmodel/gapfill.py,sha256=BPZw4sszlBhAYfHnV0pA7EpG0b2ePwS6kUfFt0Ww-ss,5159
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- gsrap/mkmodel/gapfillutils.py,sha256=XEuiX_38HBDYWOM6wVSY6UI9nuqbo9pzLOhERSt1P-g,3063
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- gsrap/mkmodel/mkmodel.py,sha256=cS8h5TTPjqzaw9jlIbb-MUfEFkHHEo59oEHItID_hvc,8506
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+ gsrap/mkmodel/gapfillutils.py,sha256=S6nFUZ1Bbdf13nVJhGK2S5C_V3hd5zwTg2o5nzejngg,3123
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+ gsrap/mkmodel/mkmodel.py,sha256=5dW5eAKW9iAFlPITM-0ZjL2FmFp3OTSvLI-xbJ-zGgs,8550
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  gsrap/mkmodel/polishing.py,sha256=R1UdFPxN8N27Iu0jsYW2N_1BkWEbBHaMYW6NkCYZK_k,3256
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  gsrap/mkmodel/pruner.py,sha256=BVOK1iFXpTgZswDgAv-TgHxKB6W3iucIAo1XWrAbu4A,7009
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  gsrap/parsedb/.ipynb_checkpoints/__init__-checkpoint.py,sha256=1k2K1gz4lIdXAwHEdJ0OhdkPu83woGv0Z4TpT1kGrTk,97
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- gsrap/parsedb/.ipynb_checkpoints/annotation-checkpoint.py,sha256=-9w1v6pSOJvQfG9BXmUigOFvHQ2qD9FF0EHoRftHiWw,4702
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- gsrap/parsedb/.ipynb_checkpoints/completeness-checkpoint.py,sha256=i9QJ_5CU8XmlHEouYo67Uxof7d8QG4imVTdkkAdQe2M,9348
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- gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py,sha256=wWhUpmvJJdFyc74RAQrPOmOT3_I6T7ZkATiIU2pglCI,16366
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+ gsrap/parsedb/.ipynb_checkpoints/annotation-checkpoint.py,sha256=Y02_zXJj_tS1GyBdfuLBy9YJjMgx3mjX6tqr1KhQ-9Q,4810
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+ gsrap/parsedb/.ipynb_checkpoints/completeness-checkpoint.py,sha256=mLK2YawP9FjR3yogHhGxF2b2ti9DKmLu9uhibsq0jy4,11064
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+ gsrap/parsedb/.ipynb_checkpoints/introduce-checkpoint.py,sha256=PuIdXvkF7gmihOEMECXVZ1V4VBOld8p3lZZ2rqXjPH8,16871
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  gsrap/parsedb/.ipynb_checkpoints/manual-checkpoint.py,sha256=F16wU8vLyM6V4F611ABuMJtwSAskL5KEgCJ7EQm_F9Y,2177
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- gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=nhpL1qVQ-yNcah7KnzS8No6tdNUz0H3cmywu6JCf6y4,7240
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- gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py,sha256=fPf9PPjy3wlEnnQJclT9qKRx0YUo2s_c4cBD21_cw_0,5493
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+ gsrap/parsedb/.ipynb_checkpoints/parsedb-checkpoint.py,sha256=tTWohNPIrw47a08ECFTyHuT4W5KlkznllIEBCpg7Kv0,7169
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+ gsrap/parsedb/.ipynb_checkpoints/repeating-checkpoint.py,sha256=9PgsSw-H84eN_dFUwK5FLgbqvydsdic4-VjCrZqkfnY,5703
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  gsrap/parsedb/__init__.py,sha256=1k2K1gz4lIdXAwHEdJ0OhdkPu83woGv0Z4TpT1kGrTk,97
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- gsrap/parsedb/annotation.py,sha256=-9w1v6pSOJvQfG9BXmUigOFvHQ2qD9FF0EHoRftHiWw,4702
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- gsrap/parsedb/completeness.py,sha256=i9QJ_5CU8XmlHEouYo67Uxof7d8QG4imVTdkkAdQe2M,9348
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- gsrap/parsedb/introduce.py,sha256=wWhUpmvJJdFyc74RAQrPOmOT3_I6T7ZkATiIU2pglCI,16366
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+ gsrap/parsedb/annotation.py,sha256=Y02_zXJj_tS1GyBdfuLBy9YJjMgx3mjX6tqr1KhQ-9Q,4810
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+ gsrap/parsedb/completeness.py,sha256=mLK2YawP9FjR3yogHhGxF2b2ti9DKmLu9uhibsq0jy4,11064
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+ gsrap/parsedb/introduce.py,sha256=PuIdXvkF7gmihOEMECXVZ1V4VBOld8p3lZZ2rqXjPH8,16871
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  gsrap/parsedb/manual.py,sha256=F16wU8vLyM6V4F611ABuMJtwSAskL5KEgCJ7EQm_F9Y,2177
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- gsrap/parsedb/parsedb.py,sha256=nhpL1qVQ-yNcah7KnzS8No6tdNUz0H3cmywu6JCf6y4,7240
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- gsrap/parsedb/repeating.py,sha256=fPf9PPjy3wlEnnQJclT9qKRx0YUo2s_c4cBD21_cw_0,5493
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+ gsrap/parsedb/parsedb.py,sha256=tTWohNPIrw47a08ECFTyHuT4W5KlkznllIEBCpg7Kv0,7169
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+ gsrap/parsedb/repeating.py,sha256=9PgsSw-H84eN_dFUwK5FLgbqvydsdic4-VjCrZqkfnY,5703
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  gsrap/runsims/.ipynb_checkpoints/__init__-checkpoint.py,sha256=6E6E1gWgH0V7ls4Omx4mxxC85gMJ_27YqhjugJzlZtY,97
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  gsrap/runsims/.ipynb_checkpoints/biosynth-checkpoint.py,sha256=fUlHUo4CfB4rGX9Dth87B1p5E5sz7i6spR7ZoqDDGaI,2836
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  gsrap/runsims/.ipynb_checkpoints/cnps-checkpoint.py,sha256=A0U8QPqW_uyrtHs99F286aEDEC6eukHXeMWrmnd0efA,5636
@@ -74,7 +76,7 @@ gsrap/runsims/.ipynb_checkpoints/essentialgenes-checkpoint.py,sha256=MzHiuaU1gwi
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  gsrap/runsims/.ipynb_checkpoints/growthfactors-checkpoint.py,sha256=r_W4idtOSJBDh7HURRsU8s1TqfOZ3TfeVw2HHDxmnGU,2265
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  gsrap/runsims/.ipynb_checkpoints/precursors-checkpoint.py,sha256=1RNt_Rxs0L1lolDmYh4_CiZgiwHfU5B_AcomJO6vJ28,2219
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  gsrap/runsims/.ipynb_checkpoints/runsims-checkpoint.py,sha256=2FC5Gs8oSYyZTjHF3A7aXB_O6myVfcn3bCxQfLJlZTk,2842
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- gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py,sha256=iHp69_0hAYylICAnuOmjYiYMlC9faKeQsuZVoLaiROo,2378
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+ gsrap/runsims/.ipynb_checkpoints/simplegrowth-checkpoint.py,sha256=tCQHTMUqum1YwlBKRTNaQoag2co_yQlCaKmISOARAlE,2353
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  gsrap/runsims/.ipynb_checkpoints/singleomission-checkpoint.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
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  gsrap/runsims/biosynth.py,sha256=fUlHUo4CfB4rGX9Dth87B1p5E5sz7i6spR7ZoqDDGaI,2836
@@ -83,10 +85,10 @@ gsrap/runsims/essentialgenes.py,sha256=MzHiuaU1gwiPdjZAgG7tkdYzkTTvoNCLp5tkezZhz
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  gsrap/runsims/growthfactors.py,sha256=r_W4idtOSJBDh7HURRsU8s1TqfOZ3TfeVw2HHDxmnGU,2265
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  gsrap/runsims/precursors.py,sha256=1RNt_Rxs0L1lolDmYh4_CiZgiwHfU5B_AcomJO6vJ28,2219
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  gsrap/runsims/runsims.py,sha256=2FC5Gs8oSYyZTjHF3A7aXB_O6myVfcn3bCxQfLJlZTk,2842
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- gsrap/runsims/simplegrowth.py,sha256=iHp69_0hAYylICAnuOmjYiYMlC9faKeQsuZVoLaiROo,2378
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+ gsrap/runsims/simplegrowth.py,sha256=tCQHTMUqum1YwlBKRTNaQoag2co_yQlCaKmISOARAlE,2353
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  gsrap/runsims/singleomission.py,sha256=jMuKAi0pINP8Jlrm-yI-tX7D110VzttR3YfTSnDRe4I,2847
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- gsrap-0.7.0.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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- gsrap-0.7.0.dist-info/METADATA,sha256=Vra-CI5I5ScraM_w59b8YsLQhXynAHj2-a40Khlm-SA,826
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- gsrap-0.7.0.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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- gsrap-0.7.0.dist-info/entry_points.txt,sha256=S9MY0DjfnbKGlZbp5bV7W6dNFy3APoEV84u9x6MV1eI,36
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- gsrap-0.7.0.dist-info/RECORD,,
90
+ gsrap-0.7.2.dist-info/LICENSE.txt,sha256=OXLcl0T2SZ8Pmy2_dmlvKuetivmyPd5m1q-Gyd-zaYY,35149
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+ gsrap-0.7.2.dist-info/METADATA,sha256=bZQ9_fiR3Fo5_mUcnWD4GgMRYtFDjO0LG74yxtjSkBs,898
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+ gsrap-0.7.2.dist-info/WHEEL,sha256=b4K_helf-jlQoXBBETfwnf4B04YC67LOev0jo4fX5m8,88
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+ gsrap-0.7.2.dist-info/entry_points.txt,sha256=S9MY0DjfnbKGlZbp5bV7W6dNFy3APoEV84u9x6MV1eI,36
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+ gsrap-0.7.2.dist-info/RECORD,,
{gsrap-0.7.0.dist-info → gsrap-0.7.2.dist-info}/WHEEL RENAMED
File without changes