def _fix_medium(args):
"""Get the fixed medium for a model."""
sid, p, growth, min_growth, max_import, mip, medium, weights = args
com = load_pickle(p)
try:
fixed = mm.complete_medium(
com,
medium,
growth=growth,
min_growth=min_growth,
max_import=max_import,
minimize_components=mip,
weights=weights
)
except Exception:
logger.error(
"Can't reach the specified growth rates for model %s." % sid
)
return None
fixed = pd.DataFrame({"reaction": fixed.index, "flux": fixed.values})
fixed["metabolite"] = [
list(com.reactions.get_by_id(r).metabolites.keys())[0].id
for r in fixed.reaction
]
fixed["description"] = [
list(com.reactions.get_by_id(r).metabolites.keys())[0].name
for r in fixed.reaction
]
fixed["sample_id"] = sid
return fixed
def _growth(args):
p, tradeoff, medium, weights, atol, rtol = args
com = load_pickle(p)
if atol is None:
atol = com.solver.configuration.tolerances.optimality
if rtol is None:
rtol = com.solver.configuration.tolerances.optimality
com = load_pickle(p)
if "glpk" in interface_to_str(com.solver.interface):
logger.error(
"Community models were not built with a QP-capable solver. "
"This means that you did not install CPLEX or Gurobi. "
"If you did install one of the two please file a bug report "
"at https://github.com/micom-dev/micom/issues."
)
return None
ex_ids = [r.id for r in com.exchanges]
logger.info(
"%d/%d import reactions found in model.",
medium.index.isin(ex_ids).sum(),
len(medium),
)
com.medium = medium[medium.index.isin(ex_ids)]
# Get growth rates
try:
sol = com.cooperative_tradeoff(fraction=tradeoff)
rates = sol.members
rates["taxon"] = rates.index
rates["tradeoff"] = tradeoff
rates["sample_id"] = com.id
except Exception:
logger.warning(
"Could not solve cooperative tradeoff for %s. "
"This can often be fixed by chosing ore permissive atol and rtol "
"arguments." % com.id)
return None
# Get the minimal medium and the solution at the same time
sol = minimal_medium(
com,
exchanges=None,
community_growth=sol.growth_rate,
min_growth=rates.growth_rate.drop("medium"),
solution=True,
weights=weights,
atol=atol,
rtol=rtol
)["solution"]
fluxes = sol.fluxes.loc[:, sol.fluxes.columns.str.startswith("EX_")].copy()
fluxes["sample_id"] = com.id
fluxes["tolerance"] = atol
anns = annotate_metabolites_from_exchanges(com)
return {"growth": rates, "exchanges": fluxes, "annotations": anns}
def _medium(args):
"""Get minimal medium for a single model."""
s, p, min_growth = args
com = load_pickle(p)
# open the bounds
for ex in com.exchanges:
ex.bounds = (-1000.0, 1000.0)
try:
medium = mm.minimal_medium(com, 0.0, min_growth=min_growth).to_frame()
except Exception:
logger.error("Could not get a minimal medium for sample %s." % s)
return None
medium.columns = ["flux"]
medium["sample_id"] = s
medium.index.name = "reaction"
return medium.reset_index()
def _tradeoff(args):
p, tradeoffs, medium = args
com = load_pickle(p)
ex_ids = [r.id for r in com.exchanges]
logger.info(
"%d/%d import reactions found in model.",
medium.index.isin(ex_ids).sum(),
len(medium),
)
com.medium = medium[medium.index.isin(ex_ids)]
try:
sol = com.optimize()
except Exception:
logger.error(
"Sample %s could not be optimized (%s)." %
(com.id, com.solver.status), )
return None
rates = sol.members
rates["taxon"] = rates.index
rates["tradeoff"] = np.nan
rates["sample_id"] = com.id
df = [rates]
# Get growth rates
try:
sol = com.cooperative_tradeoff(fraction=tradeoffs)
except Exception:
logger.warning(
"Sample %s could not be optimized with cooperative tradeoff (%s)."
% (com.id, com.solver.status), )
return None
for i, s in enumerate(sol.solution):
rates = s.members
rates["taxon"] = rates.index
rates["tradeoff"] = sol.tradeoff[i]
rates["sample_id"] = com.id
df.append(rates)
df = pd.concat(df)
return df[df.taxon != "medium"]