def _cycle_free_fva(model, reactions=None, sloppy=True, sloppy_bound=666):
"""Cycle free flux-variability analysis. (http://cran.r-project.org/web/packages/sybilcycleFreeFlux/index.html)
Parameters
----------
model : SolverBasedModel
reactions : list
List of reactions whose flux-ranges should be determined.
sloppy : boolean, optional
If true, only fluxes v with abs(v) > sloppy_bound are checked to be futile cycles (defaults to True).
sloppy_bound : int, optional
The threshold bound used by sloppy (defaults to the number of the beast).
"""
cycle_count = 0
if reactions is None:
reactions = model.reactions
else:
reactions = model._ids_to_reactions(reactions)
fva_sol = OrderedDict()
for reaction in reactions:
fva_sol[reaction.id] = dict()
model.objective = reaction
model.objective.direction = 'min'
try:
solution = model.solve()
except Unbounded:
fva_sol[reaction.id]['lower_bound'] = -numpy.inf
continue
except Infeasible:
fva_sol[reaction.id]['lower_bound'] = 0
continue
bound = solution.f
if sloppy and abs(bound) < sloppy_bound:
fva_sol[reaction.id]['lower_bound'] = bound
else:
logger.debug('Determine if {} with bound {} is a cycle'.format(
reaction.id, bound))
v0_fluxes = solution.x_dict
v1_cycle_free_fluxes = remove_infeasible_cycles(model, v0_fluxes)
if abs(v1_cycle_free_fluxes[reaction.id] - bound) < 10**-6:
fva_sol[reaction.id]['lower_bound'] = bound
else:
logger.debug('Cycle detected: {}'.format(reaction.id))
cycle_count += 1
v2_one_cycle_fluxes = remove_infeasible_cycles(
model, v0_fluxes, fix=[reaction.id])
with TimeMachine() as tm:
for key, v1_flux in six.iteritems(v1_cycle_free_fluxes):
if round(v1_flux, config.ndecimals) == 0 and round(
v2_one_cycle_fluxes[key],
config.ndecimals) != 0:
knockout_reaction = model.reactions.get_by_id(key)
knockout_reaction.knock_out(time_machine=tm)
model.objective.direction = 'min'
try:
solution = model.solve()
except Unbounded:
fva_sol[reaction.id]['lower_bound'] = -numpy.inf
except Infeasible:
fva_sol[reaction.id]['lower_bound'] = 0
else:
fva_sol[reaction.id]['lower_bound'] = solution.f
for reaction in reactions:
model.objective = reaction
model.objective.direction = 'max'
try:
solution = model.solve()
except Unbounded:
fva_sol[reaction.id]['upper_bound'] = numpy.inf
continue
except Infeasible:
fva_sol[reaction.id]['upper_bound'] = 0
continue
bound = solution.f
if sloppy and abs(bound) < sloppy_bound:
fva_sol[reaction.id]['upper_bound'] = bound
else:
logger.debug('Determine if {} with bound {} is a cycle'.format(
reaction.id, bound))
v0_fluxes = solution.x_dict
v1_cycle_free_fluxes = remove_infeasible_cycles(model, v0_fluxes)
if abs(v1_cycle_free_fluxes[reaction.id] - bound) < 1e-6:
fva_sol[reaction.id]['upper_bound'] = v0_fluxes[reaction.id]
else:
logger.debug('Cycle detected: {}'.format(reaction.id))
cycle_count += 1
v2_one_cycle_fluxes = remove_infeasible_cycles(
model, v0_fluxes, fix=[reaction.id])
with TimeMachine() as tm:
for key, v1_flux in six.iteritems(v1_cycle_free_fluxes):
if round(v1_flux, config.ndecimals) == 0 and round(
v2_one_cycle_fluxes[key],
config.ndecimals) != 0:
knockout_reaction = model.reactions.get_by_id(key)
knockout_reaction.knock_out(time_machine=tm)
model.objective.direction = 'max'
try:
solution = model.solve()
except Unbounded:
fva_sol[reaction.id]['upper_bound'] = numpy.inf
except Infeasible:
fva_sol[reaction.id]['upper_bound'] = 0
else:
fva_sol[reaction.id]['upper_bound'] = solution.f
df = pandas.DataFrame.from_dict(fva_sol, orient='index')
lb_higher_ub = df[df.lower_bound > df.upper_bound]
# Assert that these cases really only numerical artifacts
assert ((lb_higher_ub.lower_bound - lb_higher_ub.upper_bound) < 1e-6).all()
df.lower_bound[lb_higher_ub.index] = df.upper_bound[lb_higher_ub.index]
return df
def _cycle_free_fva(model, reactions=None, sloppy=True, sloppy_bound=666):
"""Cycle free flux-variability analysis. (http://cran.r-project.org/web/packages/sybilcycleFreeFlux/index.html)
Parameters
----------
model : SolverBasedModel
reactions : list
List of reactions whose flux-ranges should be determined.
sloppy : boolean, optional
If true, only fluxes v with abs(v) > sloppy_bound are checked to be futile cycles (defaults to True).
sloppy_bound : int, optional
The threshold bound used by sloppy (defaults to the number of the beast).
"""
cycle_count = 0
if reactions is None:
reactions = model.reactions
else:
reactions = model._ids_to_reactions(reactions)
fva_sol = OrderedDict()
for reaction in reactions:
fva_sol[reaction.id] = dict()
model.objective = reaction
model.objective.direction = 'min'
try:
solution = model.solve()
except Unbounded:
fva_sol[reaction.id]['lower_bound'] = -numpy.inf
continue
except Infeasible:
fva_sol[reaction.id]['lower_bound'] = 0
continue
bound = solution.f
if sloppy and abs(bound) < sloppy_bound:
fva_sol[reaction.id]['lower_bound'] = bound
else:
logger.debug('Determine if {} with bound {} is a cycle'.format(reaction.id, bound))
v0_fluxes = solution.x_dict
v1_cycle_free_fluxes = remove_infeasible_cycles(model, v0_fluxes)
if abs(v1_cycle_free_fluxes[reaction.id] - bound) < 10 ** -6:
fva_sol[reaction.id]['lower_bound'] = bound
else:
logger.debug('Cycle detected: {}'.format(reaction.id))
cycle_count += 1
v2_one_cycle_fluxes = remove_infeasible_cycles(model, v0_fluxes, fix=[reaction.id])
with TimeMachine() as tm:
for key, v1_flux in six.iteritems(v1_cycle_free_fluxes):
if round(v1_flux, config.ndecimals) == 0 and round(v2_one_cycle_fluxes[key],
config.ndecimals) != 0:
knockout_reaction = model.reactions.get_by_id(key)
knockout_reaction.knock_out(time_machine=tm)
model.objective.direction = 'min'
try:
solution = model.solve()
except Unbounded:
fva_sol[reaction.id]['lower_bound'] = -numpy.inf
except Infeasible:
fva_sol[reaction.id]['lower_bound'] = 0
else:
fva_sol[reaction.id]['lower_bound'] = solution.f
for reaction in reactions:
model.objective = reaction
model.objective.direction = 'max'
try:
solution = model.solve()
except Unbounded:
fva_sol[reaction.id]['upper_bound'] = numpy.inf
continue
except Infeasible:
fva_sol[reaction.id]['upper_bound'] = 0
continue
bound = solution.f
if sloppy and abs(bound) < sloppy_bound:
fva_sol[reaction.id]['upper_bound'] = bound
else:
logger.debug('Determine if {} with bound {} is a cycle'.format(reaction.id, bound))
v0_fluxes = solution.x_dict
v1_cycle_free_fluxes = remove_infeasible_cycles(model, v0_fluxes)
if abs(v1_cycle_free_fluxes[reaction.id] - bound) < 1e-6:
fva_sol[reaction.id]['upper_bound'] = v0_fluxes[reaction.id]
else:
logger.debug('Cycle detected: {}'.format(reaction.id))
cycle_count += 1
v2_one_cycle_fluxes = remove_infeasible_cycles(model, v0_fluxes, fix=[reaction.id])
with TimeMachine() as tm:
for key, v1_flux in six.iteritems(v1_cycle_free_fluxes):
if round(v1_flux, config.ndecimals) == 0 and round(v2_one_cycle_fluxes[key],
config.ndecimals) != 0:
knockout_reaction = model.reactions.get_by_id(key)
knockout_reaction.knock_out()
model.objective.direction = 'max'
try:
solution = model.solve()
except Unbounded:
fva_sol[reaction.id]['upper_bound'] = numpy.inf
except Infeasible:
fva_sol[reaction.id]['upper_bound'] = 0
else:
fva_sol[reaction.id]['upper_bound'] = solution.f
df = pandas.DataFrame.from_dict(fva_sol, orient='index')
lb_higher_ub = df[df.lower_bound > df.upper_bound]
# Assert that these cases really only numerical artifacts
assert ((lb_higher_ub.lower_bound - lb_higher_ub.upper_bound) < 1e-6).all()
df.lower_bound[lb_higher_ub.index] = df.upper_bound[lb_higher_ub.index]
return df