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('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): # 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) self.solver = cplex.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': 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| <=>')) 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('|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 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]| =>')) 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('|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): # 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[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('=> (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): # TODO use mock model instead of actual model 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.model = MetabolicModel.load_model(self.database, self.database.reactions) self.solver = cplex.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|')) 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('=> (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.model = MetabolicModel.load_model( self.database, self.database.reactions) self.solver = cplex.Solver()
def setUp(self): # TODO use mock model instead of actual model 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) self.solver = cplex.Solver()
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[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): # 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): 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): 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): 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.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 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): # 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 self.solver = cplex.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|')) 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) 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('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('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('|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')