def setUp(self):
database1 = DictDatabase()
database1.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
database1.set_reaction('rxn_2', parse_reaction('|B| => |C| + |D|'))
database1.set_reaction('rxn_3', parse_reaction('|D| <=> |E|'))
database1.set_reaction('rxn_4', parse_reaction('|F| => |G|'))
database2 = DictDatabase()
database2.set_reaction('rxn_2', parse_reaction('|B| => |C|'))
database2.set_reaction('rxn_3', parse_reaction('|C| => |D|'))
database2.set_reaction('rxn_4', parse_reaction('|F| <=> |G|'))
database2.set_reaction('rxn_5', parse_reaction('|G| + |I| <=> |H|'))
self.database = ChainedDatabase(database2, database1)
def setUp(self):
self._database = DictDatabase()
self._database.set_reaction('rxn_1', parse_reaction('A[e] => B[e]'))
self._database.set_reaction('rxn_2', parse_reaction('B[e] => C[e]'))
self._database.set_reaction('rxn_3', parse_reaction('B[e] <=> D[e]'))
self._database.set_reaction('rxn_4', parse_reaction('C[e] <=> E[e]'))
self._database.set_reaction('rxn_5', parse_reaction('D[e] => E[e]'))
self._database.set_reaction('rxn_6', parse_reaction('E[e] =>'))
self._database.set_reaction('ex_A', parse_reaction('A[e] <=>'))
self._mm = MetabolicModel.load_model(
self._database, self._database.reactions)
self._assoc = {
'rxn_1': str('gene_1'),
'rxn_2': str('gene_2'),
'rxn_3': str('gene_5'),
'rxn_4': str('gene_3 or gene_4'),
'rxn_5': str('gene_5 and gene_6')
}
self._obj_reaction = 'rxn_6'
try:
self._solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')
try:
self.solver = generic.Solver(integer=True)
except generic.RequirementsError:
self.skipTest('Needs and integer programming solver')
def setUp(self):
self._database = DictDatabase()
self._database.set_reaction('rxn_1', parse_reaction('A[e] => B[e]'))
self._database.set_reaction('rxn_2', parse_reaction('B[e] => C[e]'))
self._database.set_reaction('rxn_3', parse_reaction('B[e] => D[e]'))
self._database.set_reaction('rxn_4', parse_reaction('C[e] => E[e]'))
self._database.set_reaction('rxn_5', parse_reaction('D[e] => E[e]'))
self._database.set_reaction('rxn_6', parse_reaction('E[e] =>'))
self._database.set_reaction('ex_A', parse_reaction('A[e] <=>'))
self._mm = MetabolicModel.load_model(self._database,
self._database.reactions)
self._assoc = {
'rxn_1': boolean.Expression('gene_1'),
'rxn_2': boolean.Expression('gene_2 or gene_3'),
'rxn_5': boolean.Expression('gene_3 and gene_4')
}
self._obj_reaction = 'rxn_6'
try:
self._solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')
self._prob = fluxanalysis.FluxBalanceProblem(self._mm, self._solver)
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> 2 A'))
self.database.set_reaction('rxn_2', parse_reaction('A <=> B'))
self.database.set_reaction('rxn_3', parse_reaction('A => D[e]'))
self.database.set_reaction('rxn_4', parse_reaction('A + 2 B => C'))
self.database.set_reaction('rxn_5', parse_reaction('C => 3 D[e]'))
self.database.set_reaction('rxn_6', parse_reaction('D[e] =>'))
def test_load_model_with_reaction_subset(self):
database = DictDatabase()
database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
database.set_reaction('rxn_2', parse_reaction('|B| => |C|'))
database.set_reaction('rxn_3', parse_reaction('|C| => |D|'))
model = MetabolicModel.load_model(database, {'rxn_1'})
self.assertEqual(set(model.reactions), {'rxn_1'})
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D[e]|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D[e]|'))
self.database.set_reaction('rxn_6', parse_reaction('|D[e]| =>'))
def setUp(self):
self._database = DictDatabase()
self._database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
self._database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self._database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
self._database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
self._mm = MetabolicModel.load_model(self._database,
self._database.reactions)
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D[e]|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D[e]|'))
self.database.set_reaction('rxn_6', parse_reaction('|D[e]| =>'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
def setUp(self):
self._database = DictDatabase()
self._database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
self._database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self._database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
self._database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
self._mm = MetabolicModel.load_model(self._database,
self._database.reactions)
self._strategy = randomsparse.ReactionDeletionStrategy(self._mm)
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) A[c]'))
self.database.set_reaction('rxn_2', parse_reaction('A[c] <=> B[c]'))
self.database.set_reaction('rxn_3', parse_reaction('A[c] => D[e]'))
self.database.set_reaction('rxn_4', parse_reaction('A[c] => C[c]'))
self.database.set_reaction('rxn_5', parse_reaction('C[c] => D[e]'))
self.database.set_reaction('rxn_6', parse_reaction('D[e] =>'))
self.model = MetabolicModel.load_model(self.database,
self.database.reactions)
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('|A| + |B| => |C|'))
self.database.set_reaction('rxn_2',
parse_reaction('|C| + |Z| => |A| + |B|'))
self.model = MetabolicModel.load_model(self.database,
self.database.reactions)
try:
self.solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')
def setUp(self):
# TODO use mock database instead of actual database
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))
model = MetabolicModel.load_model(self.database, self.database.reactions)
self.model = FlipableModelView(model)
def setUp(self):
self._database = DictDatabase()
self._database.set_reaction('rxn_1', parse_reaction('|A| <=>'))
self._database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self._database.set_reaction('rxn_3', parse_reaction('|C| <=> |B|'))
self._database.set_reaction('rxn_4', parse_reaction('|C| <=>'))
self._mm = MetabolicModel.load_model(self._database,
self._database.reactions)
self._assoc = {'rxn_2': boolean.Expression('gene_1 or gene_2')}
self._strategy = randomsparse.GeneDeletionStrategy(
self._mm, self._assoc)
def setUp(self):
# TODO use mock model instead of actual model
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> |A|'))
self.database.set_reaction('rxn_2',
parse_reaction('(0.000001) |A| =>'))
self.model = MetabolicModel.load_model(self.database,
self.database.reactions)
try:
self.solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_4', parse_reaction('|C| => |D|'))
self.database.set_reaction('rxn_5', parse_reaction('|D| <=> |E|'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
try:
self.solver = generic.Solver(integer=True)
except generic.RequirementsError:
self.skipTest('Unable to find an MILP solver for tests')
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> |A|'))
self.database.set_reaction('rxn_2',
parse_reaction('(0.000001) |A| =>'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
try:
self.solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')
# Skip these tests with GLPK because of issue #61.
if self.solver.properties['name'] == 'glpk':
self.skipTest('Test has known issue with GLPK')
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('ex_A', parse_reaction('|A| <=>'))
self.database.set_reaction('ex_D', parse_reaction('|D| <=>'))
self.database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
self.database.set_reaction('rxn_2', parse_reaction('|B| <=> |C|'))
self.database.set_reaction('rxn_3', parse_reaction('|C| <=> |D|'))
self.database.set_reaction('rxn_4', parse_reaction('|D| <=> |E|'))
self.database.set_reaction('rxn_5', parse_reaction('|E| => |B|'))
self.model = MetabolicModel.load_model(self.database,
self.database.reactions)
self.model.limits['ex_A'].lower = -10 # Low uptake
self.model.limits['ex_D'].lower = 0 # No uptake
try:
self.solver = generic.Solver(integer=True)
except generic.RequirementsError:
self.skipTest('Unable to find an MILP solver for tests')
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('=> (2) |A|'))
self.database.set_reaction('rxn_2', parse_reaction('|A| <=> |B|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |D|'))
self.database.set_reaction('rxn_4', parse_reaction('|A| => |C|'))
self.database.set_reaction('rxn_5', parse_reaction('|C| => |D|'))
self.database.set_reaction('rxn_6', parse_reaction('|D| =>'))
self.database.set_reaction('rxn_7', parse_reaction('|E| => |F|'))
self.database.set_reaction('rxn_8', parse_reaction('|F| => |E|'))
self.model = MetabolicModel.load_model(self.database,
self.database.reactions)
self.model.limits['rxn_5'].upper = 100
try:
self.solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')
def setUp(self):
self.database = DictDatabase()
self.database.set_reaction('rxn_1', parse_reaction('|A| => |B|'))
self.database.set_reaction('rxn_2', parse_reaction('|B| => |G|'))
self.database.set_reaction('rxn_3', parse_reaction('|A| => |G|'))
self.database.set_reaction('rxn_4', parse_reaction('|B| => |H|'))
self.database.set_reaction('rxn_5', parse_reaction('|B| => |C| + |F|'))
self.database.set_reaction('rxn_6', parse_reaction('|C| => |D|'))
self.database.set_reaction('rxn_7', parse_reaction('|E| <=> |D|'))
self.database.set_reaction('rxn_9', parse_reaction('|I| => |J|'))
self.database.set_reaction('rxn_10', parse_reaction('|J| => |K|'))
self.database.set_reaction('rxn_A', parse_reaction('=> |A|'))
self.database.set_reaction('rxn_G', parse_reaction('|G| =>'))
self.database.set_reaction('rxn_E', parse_reaction('|E| =>'))
self.database.set_reaction(
'rxn_bio', parse_reaction('|D| + (2.5) |F| =>'))
self.model = MetabolicModel.load_model(
self.database, self.database.reactions)
try:
self.solver = generic.Solver()
except generic.RequirementsError:
self.skipTest('Unable to find an LP solver for tests')
