def test_grow(tmp_path):
data = md.test_data()
built = build(data, db, str(tmp_path), cutoff=0)
grown = grow(built, str(tmp_path), medium, 0.5)
assert len(grown) == 3
assert "growth_rate" in grown.growth_rates.columns
assert "flux" in grown.exchanges.columns
with pytest.raises(OptimizationError):
grow(built, str(tmp_path), medium, 1.5)
def grow(models: CommunityModelDirectory,
medium: pd.DataFrame,
tradeoff: float = 0.5,
threads: int = 1,
strategy: str = "pFBA") -> mw.core.GrowthResults:
"""Simulate growth for a set of community models."""
if strategy == "minimal uptake":
strategy = "minimal imports"
model_folder = str(models.model_files.path_maker(model_id="blub")).replace(
"blub.pickle", "")
manifest = models.manifest.view(pd.DataFrame)
results = mw.grow(manifest,
model_folder,
medium,
tradeoff,
threads,
strategy=strategy)
return results
# save this community to file (Can I save one pickle file per GEM?)
comm_fp = model_path + "/" + sample + "_community.pickle"
com.to_pickle(comm_fp)
#load it:
# com = load_pickle("1_interm_files/community.pickle")
# see exchanges:
#com.exchanges
print("\n simulating growth\n")
#############################
# SIMULATE GROWTH
comm_filename = sample + "_community.pickle"
manifest = pd.DataFrame({
"sample_id": sample,
"file": comm_filename
},
index=[0])
res = grow(manifest, model_path, medium=medium, tradeoff=0.5, threads=12)
res.exchanges
## save to file:
out_fp = "exchanges_grow_" + sample + ".csv"
outfile = open(out_fp, "w")
res.exchanges.to_csv(outfile)
outfile.close()
print("\nDONE!!\n")
def growth_data(tmp_path):
"""Generate some growth simulation data."""
data = md.test_data()
built = build(data, md.test_db, str(tmp_path), cutoff=0)
grown = grow(built, str(tmp_path), medium, 0.5)
return grown
manifest = pd.DataFrame({
"sample_id": sample,
"file": comm_filename
},
index=[0])
# Medium (western diet, after diluting nutrients absorbed in the small intestine)
med = pd.DataFrame(com.medium.items(), columns=['reaction', 'flux'])
# test increasing flux
med['flux'] = med['flux'] * 6
# grow!! using parsimonious FBA
res = grow(manifest,
pickles_path,
medium=med,
tradeoff=trade_off,
threads=th,
strategy="pFBA")
res.exchanges
# divide fluxes by the 600 (100 added in the build_comm_models, multiplied by 6 here)
res.exchanges['flux'] = res.exchanges['flux'] / 600
## add sample name:
res.exchanges['sample_id'] = sample
res.growth_rates['sample_id'] = sample
## save to file:
out_fp_exc = out_dir + "/" + "exchanges_grow_" + sample + ".csv"
outfile = open(out_fp_exc, "w")
res.exchanges.to_csv(out_fp_exc)