def test_complicated_model():
"""Test a complicated model.
Difficult model since the online mean calculation is numerically
unstable so many samples weakly violate the equality constraints.
"""
model = Model('flux_split')
reaction1 = Reaction('V1')
reaction2 = Reaction('V2')
reaction3 = Reaction('V3')
reaction1.bounds = (0, 6)
reaction2.bounds = (0, 8)
reaction3.bounds = (0, 10)
A = Metabolite('A')
reaction1.add_metabolites({A: -1})
reaction2.add_metabolites({A: -1})
reaction3.add_metabolites({A: 1})
model.add_reactions([reaction1, reaction2, reaction3])
optgp = OptGPSampler(model, 1, seed=42)
achr = ACHRSampler(model, seed=42)
optgp_samples = optgp.sample(100)
achr_samples = achr.sample(100)
assert any(optgp_samples.corr().abs() < 1.0)
assert any(achr_samples.corr().abs() < 1.0)
# > 95% are valid
assert sum(optgp.validate(optgp_samples) == "v") > 95
assert sum(achr.validate(achr_samples) == "v") > 95
def test_find_boundary_types_sink(model: Model) -> None:
"""Test boundary type identification for sinks."""
sn = Reaction("sink")
model.add_reaction(sn)
sn.build_reaction_from_string("atp_c <->")
sn.bounds = -1000, 1000
sn = model.sinks
assert len(sn) == 1
assert "sink" in [r.id for r in sn]
def add_bigg_reactions(bigg_list, model, ignore_pseudo_reactions=True):
""" Create a COBRA reaction from a BiGG reaction.
Parameters
----------
bigg_list : list of dict
List of dictionaries with BiGG reaction data
model : cobra.core.Model
Model to add reactions to
ignore_pseudo_reactions : bool, optional
When True, do not include pseudo reactions
"""
# Create a Reaction object for each BiGG reaction.
reactions = DictList()
for bigg_reaction in bigg_list:
if bigg_reaction['pseudoreaction'] and ignore_pseudo_reactions:
continue
reaction = Reaction(id=bigg_reaction['bigg_id'],
name=bigg_reaction['name'])
reaction.notes['aliases'] = bigg_reaction['database_links']
metabolites = dict()
for met in bigg_reaction['metabolites']:
metabolite = model.metabolites.get_by_id('{0}_{1}'.format(
met['bigg_id'], met['compartment_bigg_id']))
metabolites[metabolite] = met['stoichiometry']
reaction.add_metabolites(metabolites)
try:
reaction.bounds = (bigg_reaction['results'][0]['lower_bound'],
bigg_reaction['results'][0]['upper_bound'])
except KeyError:
if '⇌' in bigg_reaction['reaction_string']:
reaction.bounds = (-1000.0, 1000.0)
else:
warn('Unknown direction symbol in reaction string {0}'.format(
bigg_reaction['reaction_string']))
reactions.append(reaction)
# Add all of the reactions to the model.
model.add_reactions(reactions)
return
def test_complicated_model():
"""Test a complicated model.
Difficult model since the online mean calculation is numerically
unstable so many samples weakly violate the equality constraints.
"""
model = Model('flux_split')
reaction1 = Reaction('V1')
reaction2 = Reaction('V2')
reaction3 = Reaction('V3')
reaction1.bounds = (0, 6)
reaction2.bounds = (0, 8)
reaction3.bounds = (0, 10)
A = Metabolite('A')
reaction1.add_metabolites({A: -1})
reaction2.add_metabolites({A: -1})
reaction3.add_metabolites({A: 1})
model.add_reactions([reaction1, reaction2, reaction3])
optgp = OptGPSampler(model, 1, seed=42)
achr = ACHRSampler(model, seed=42)
optgp_samples = optgp.sample(100)
achr_samples = achr.sample(100)
assert any(optgp_samples.corr().abs() < 1.0)
assert any(achr_samples.corr().abs() < 1.0)
# > 95% are valid
assert sum(optgp.validate(optgp_samples) == "v") > 95
assert sum(achr.validate(achr_samples) == "v") > 95
def test_model_medium(self, model):
# Add a dummy 'malformed' import reaction
bad_import = Reaction('bad_import')
bad_import.add_metabolites({model.metabolites.pyr_c: 1})
bad_import.bounds = (0, 42)
model.add_reaction(bad_import)
# Test basic setting and getting methods
medium = model.medium
model.medium = medium
assert model.medium == medium
# Test context management
with model:
# Ensure the bounds are correct beforehand
assert model.reactions.EX_glc__D_e.lower_bound == -10
assert model.reactions.bad_import.upper_bound == 42
assert model.reactions.EX_co2_e.lower_bound == -1000
# Make changes to the media
new_medium = model.medium
new_medium['EX_glc__D_e'] = 20
new_medium['bad_import'] = 24
del new_medium['EX_co2_e']
# Change the medium, make sure changes work
model.medium = new_medium
assert model.reactions.EX_glc__D_e.lower_bound == -20
assert model.reactions.bad_import.upper_bound == 24
assert model.reactions.EX_co2_e.lower_bound == 0
# Make sure changes revert after the contex
assert model.reactions.EX_glc__D_e.lower_bound == -10
assert model.reactions.bad_import.upper_bound == 42
assert model.reactions.EX_co2_e.lower_bound == -1000
new_medium['bogus_rxn'] = 0
with pytest.raises(KeyError):
model.medium = new_medium
def test_model_medium(self, model):
# Add a dummy 'malformed' import reaction
bad_import = Reaction('bad_import')
bad_import.add_metabolites({model.metabolites.pyr_c: 1})
bad_import.bounds = (0, 42)
model.add_reaction(bad_import)
# Test basic setting and getting methods
medium = model.medium
model.medium = medium
assert model.medium == medium
# Test context management
with model:
# Ensure the bounds are correct beforehand
assert model.reactions.EX_glc__D_e.lower_bound == -10
assert model.reactions.bad_import.upper_bound == 42
assert model.reactions.EX_co2_e.lower_bound == -1000
# Make changes to the media
new_medium = model.medium
new_medium['EX_glc__D_e'] = 20
new_medium['bad_import'] = 24
del new_medium['EX_co2_e']
# Change the medium, make sure changes work
model.medium = new_medium
assert model.reactions.EX_glc__D_e.lower_bound == -20
assert model.reactions.bad_import.upper_bound == 24
assert model.reactions.EX_co2_e.lower_bound == 0
# Make sure changes revert after the contex
assert model.reactions.EX_glc__D_e.lower_bound == -10
assert model.reactions.bad_import.upper_bound == 42
assert model.reactions.EX_co2_e.lower_bound == -1000
new_medium['bogus_rxn'] = 0
with pytest.raises(KeyError):
model.medium = new_medium
def test_make_lhs_irreversible_reversible(model: Model) -> None:
"""Test reaction LHS irreversibility to reversibility."""
rxn = Reaction("test")
rxn.add_metabolites({
model.metabolites[0]: -1.0,
model.metabolites[1]: 1.0
})
rxn.bounds = (-1000.0, -100)
model.add_reaction(rxn)
assert rxn.lower_bound == -1000.0
assert rxn.upper_bound == -100.0
assert rxn.forward_variable.lb == 0.0
assert rxn.forward_variable.ub == 0.0
assert rxn.reverse_variable.lb == 100.0
assert rxn.reverse_variable.ub == 1000.0
rxn.upper_bound = 666.0
assert rxn.lower_bound == -1000.0
assert rxn.upper_bound == 666.0
assert rxn.forward_variable.lb == 0.0
assert rxn.forward_variable.ub == 666
assert rxn.reverse_variable.lb == 0.0
assert rxn.reverse_variable.ub == 1000.0