def test_medium_mip(self, model):
med = medium.minimal_medium(model, 0.8, minimize_components=True)
assert len(med) <= 4
assert all(med > 1e-6)
# Anaerobic growth
med = medium.minimal_medium(model, 0.1, minimize_components=True)
assert len(med) <= 3
assert all(med > 1e-6)
def test_medium_mip(self, model):
med = medium.minimal_medium(model, 0.8, minimize_components=True)
assert len(med) <= 4
assert all(med > 1e-6)
# Anaerobic growth
med = medium.minimal_medium(model, 0.1, minimize_components=True)
assert len(med) <= 3
assert all(med > 1e-6)
def test_open_exchanges(self, model):
model.reactions.EX_glc__D_e.bounds = 0, 0
med = medium.minimal_medium(model, 0.8)
assert med is None
med = medium.minimal_medium(model, 0.8, minimize_components=True)
assert med is None
med = medium.minimal_medium(model, 0.8, open_exchanges=True)
assert len(med) >= 3
med = medium.minimal_medium(model, 0.8, open_exchanges=100)
assert len(med) >= 3
def test_open_exchanges(self, model):
model.reactions.EX_glc__D_e.bounds = 0, 0
med = medium.minimal_medium(model, 0.8)
assert med is None
med = medium.minimal_medium(model, 0.8, minimize_components=True)
assert med is None
med = medium.minimal_medium(model, 0.8, open_exchanges=True)
assert len(med) >= 3
med = medium.minimal_medium(model, 0.8, open_exchanges=100)
assert len(med) >= 3
def __init__(self, config={}):
model_path = config.get('model_path')
# get tolerances
self.default_tolerance = config.get('default_tolerance', [0.95, 1])
self.tolerance = config.get('tolerance', {})
# set MOMA (minimization of metabolic adjustment)
self.moma = config.get('moma', False)
if model_path:
# load a BiGG model
self.model = cobra.io.load_json_model(model_path)
swap_synonyms(self.model)
extract = extract_model(self.model)
self.stoichiometry = extract['stoichiometry']
self.reversible = extract['reversible']
self.external_molecules = extract['external_molecules']
self.objective = extract['objective']
self.flux_bounds = extract['flux_bounds']
self.molecular_weights = extract['molecular_weights']
self.exchange_bounds = extract['exchange_bounds']
self.default_upper_bound = DEFAULT_UPPER_BOUND # TODO -- can this be extracted from model?
self.flux_scaling = extract['flux_scaling']
else:
# create an FBA model from config
self.stoichiometry = config['stoichiometry']
self.reversible = config.get('reversible', [])
self.external_molecules = config['external_molecules']
self.objective = config['objective']
self.flux_bounds = config.get('flux_bounds', {})
self.molecular_weights = config.get('molecular_weights', {})
self.exchange_bounds = config.get('exchange_bounds', {})
self.default_upper_bound = config.get('default_upper_bound',
DEFAULT_UPPER_BOUND)
self.flux_scaling = config.get('flux_scaling', 1)
self.model = build_model(self.stoichiometry, self.reversible,
self.objective, self.external_molecules,
self.default_upper_bound)
# apply constraints
self.constrain_reaction_bounds(self.flux_bounds)
self.set_exchange_bounds()
self.exchange_bounds_keys = list(self.exchange_bounds.keys())
# get minimal external state
# TODO -- make sure that scaling is accounted for
max_growth = self.model.slim_optimize()
max_exchange = minimal_medium(self.model, max_growth)
self.minimal_external = {
ex[len(EXTERNAL_PREFIX):len(ex)]: value
for ex, value in max_exchange.items()
}
# initialize solution
self.solution = self.model.optimize()
def test_medium_exports(self, model):
med = medium.minimal_medium(model,
0.8,
exports=True,
minimize_components=True)
assert len(med) > 4
assert any(med < -1e-6)
def test_medium_alternative_mip(self, model):
med = medium.minimal_medium(model, 0.8, minimize_components=5,
open_exchanges=True)
assert isinstance(med, pd.DataFrame)
assert med.shape[0] >= 5
assert med.shape[1] == 5
assert all((med > 0).sum() == 3)
assert all(med.sum(axis=1) > 1e-6)
def test_medium_alternative_mip(self, model):
med = medium.minimal_medium(model, 0.8, minimize_components=5,
open_exchanges=True)
assert isinstance(med, pd.DataFrame)
assert med.shape[0] >= 5
assert med.shape[1] == 5
assert all((med > 0).sum() == 3)
assert all(med.sum(axis=1) > 1e-6)
def minimal_external(self):
'''get minimal external state'''
max_growth = self.model.slim_optimize()
max_exchange = minimal_medium(self.model, max_growth)
return {
ex[len(EXTERNAL_PREFIX):len(ex)]: value
for ex, value in max_exchange.items()
}
def test_medium_linear(self, model):
med = medium.minimal_medium(model, 0.8)
assert len(med) <= 4
assert all(med > 1e-6)
def test_medium_exports(self, model):
med = medium.minimal_medium(model, 0.8, exports=True,
minimize_components=True)
assert len(med) > 4
assert any(med < -1e-6)
def test_medium_linear(self, model):
med = medium.minimal_medium(model, 0.8)
assert len(med) <= 4
assert all(med > 1e-6)
def deter_milieu_minimal(self):
from cobra.medium import minimal_medium
self.deter_les_croissances()
self.milieu_minimal=dict(minimal_medium(self.bacterie.model, self.croissance_global_max))
def deter_milieu_minimal(self):
from cobra.medium import minimal_medium
self.milieu_minimal=minimal_medium(self.model, self.croissance_global_max)
