def test_load_glpk_cmd(self):
solver = load_pulp_solver(solver_names=['GLPK_CMD'])
if not solver:
self.skipTest("GLPK_CMD is not available!")
else:
self.assertListEqual(GLPK_CMD_OPTIONS, solver.options)
def test_load_scip_cmd(self):
solver = load_pulp_solver(solver_names=['SCIP_CMD'])
if not solver:
self.skipTest("SCIP_CMD is not available!")
else:
self.assertIn("-s", solver.options)
def test_optstoic_glycolysis():
logger = create_logger(name='optstoicpy.script.optstoic_glycolysis.main')
#logger.debug('Testing optstoic output filepath: %s', res_dir)
logger.info("Test optstoic_glycolysis")
pulp_solver = load_pulp_solver(
solver_names=[
'SCIP_CMD',
'GUROBI',
'GUROBI_CMD',
'CPLEX_CMD',
'GLPK_CMD'],
logger=logger)
test = OptStoicGlycolysis(
objective='MinFlux',
nATP=1,
zlb=10, # setting this may slow down the optimization, but integer cut constraints will work
max_iteration=1,
pulp_solver=pulp_solver,
result_filepath='./result/',
M=1000,
logger=logger)
if sys.platform == 'cygwin':
lp_prob, pathways = test.solve_gurobi_cl(
outputfile='test_optstoic_cyg.txt', cleanup=False)
#test.max_iteration = test.max_iteration + 2
#lp_prob, pathways = test.solve_gurobi_cl(outputfile='test_optstoic_cyg.txt', exclude_existing_solution=True, cleanup=False)
else:
lp_prob, pathways = test.solve(outputfile='test_optstoic.txt')
#test.max_iteration = test.max_iteration + 1
#lp_prob, pathways = test.solve(outputfile='test_optstoic.txt', exclude_existing_solution=True)
return lp_prob, pathways
def test_optstoic():
"""An alternative to the nosetest due to issue with PULP/SCIP_CMD
"""
logger = create_logger(name='optstoicpy.script.optstoic.main')
logger.info("Test generalized optstoic")
# Set the following reactions as allowable export reactions
db3 = load_db_v3(reduce_model_size=True,
user_defined_export_rxns_Sji={
'EX_glc': {
'C00031': -1.0
},
'EX_nad': {
'C00003': -1.0
},
'EX_adp': {
'C00008': -1.0
},
'EX_phosphate': {
'C00009': -1.0
},
'EX_pyruvate': {
'C00022': -1.0
},
'EX_nadh': {
'C00004': -1.0
},
'EX_atp': {
'C00002': -1.0
},
'EX_h2o': {
'C00001': -1.0
},
'EX_hplus': {
'C00080': -1.0
},
'EX_nadp': {
'C00006': -1.0
},
'EX_nadph': {
'C00005': -1.0
}
})
#logger.debug('Testing optstoic output filepath: %s', res_dir)
pulp_solver = load_pulp_solver(solver_names=[
'SCIP_CMD', 'GUROBI', 'GUROBI_CMD', 'CPLEX_CMD', 'GLPK_CMD'
],
logger=logger)
# How to add custom flux constraints:
# E.g.,
# v('EX_nadph') + v('EX_nadh') = 2;
# v('EX_nadp') + v('EX_nad') = -2;
# v('EX_nadh') + v('EX_nad') = 0;
# v('EX_nadph') + v('EX_nadp') = 0;
# became
# lp_prob += v['EX_nadph'] + v['EX_nadh'] == 2, 'nadphcons1'
# lp_prob += v['EX_nadp'] + v['EX_nad'] == -2, 'nadphcons2'
# lp_prob += v['EX_nadh'] + v['EX_nad'] == 0, 'nadphcons3'
# lp_prob += v['EX_nadph'] + v['EX_nadp'] == 0, 'nadphcons4'
custom_flux_constraints = [{
'constraint_name': 'nadphcons1',
'reactions': ['EX_nadph', 'EX_nadh'],
'UB': 2,
'LB': 2
}, {
'constraint_name': 'nadphcons2',
'reactions': ['EX_nadp', 'EX_nad'],
'UB': -2,
'LB': -2
}, {
'constraint_name': 'nadphcons3',
'reactions': ['EX_nadh', 'EX_nad'],
'UB': 0,
'LB': 0
}, {
'constraint_name': 'nadphcons4',
'reactions': ['EX_nadph', 'EX_nadp'],
'UB': 0,
'LB': 0
}]
specific_bounds = {
'EX_glc': {
'LB': -1,
'UB': -1
},
'EX_pyruvate': {
'LB': 2,
'UB': 2
},
'EX_nad': {
'LB': -2,
'UB': 0
},
'EX_nadh': {
'LB': 0,
'UB': 2
},
'EX_nadp': {
'LB': -2,
'UB': 0
},
'EX_nadph': {
'LB': 0,
'UB': 2
},
'EX_adp': {
'LB': -1,
'UB': -1
},
'EX_phosphate': {
'LB': -1,
'UB': -1
},
'EX_atp': {
'LB': 1,
'UB': 1
},
'EX_h2o': {
'LB': 1,
'UB': 1
},
'EX_hplus': {
'LB': -10,
'UB': 10
}
} # pulp/gurobi has issue with "h+"
test = OptStoic(database=db3,
objective='MinFlux',
zlb=None,
specific_bounds=specific_bounds,
custom_flux_constraints=custom_flux_constraints,
add_loopless_constraints=True,
max_iteration=2,
pulp_solver=pulp_solver,
result_filepath='./result/',
M=1000,
logger=logger)
if sys.platform == 'cygwin':
lp_prob, pathways = test.solve_gurobi_cl(
outputfile='test_optstoic_cyg.txt', cleanup=False)
#test.max_iteration = test.max_iteration + 2
#lp_prob, pathways = test.solve_gurobi_cl(outputfile='test_optstoic_cyg.txt', exclude_existing_solution=True, cleanup=False)
else:
lp_prob, pathways = test.solve(outputfile='test_optstoic.txt')
#test.max_iteration = test.max_iteration + 1
#lp_prob, pathways = test.solve(outputfile='test_optstoic.txt', exclude_existing_solution=True)
return lp_prob, pathways
def test_at_least_one_pulp_solver_loading(self):
pulp_solver = load_pulp_solver(solver_names=ORDERED_SOLVERS)
self.assertNotEqual(pulp_solver, None)
self.assertIn(pulp_solver.name, ORDERED_SOLVERS)
def setUp(self):
self.logger = create_logger(name='Test generalized optstoic')
self.pulp_solver = load_pulp_solver(solver_names=ORDERED_SOLVERS)
if self.pulp_solver.name not in ['GUROBI', 'GUROBI_CMD', 'CPLEX_CMD']:
self.skipTest("Skip because it will take a long time to solve.")
def test_blocked_reactions_analysis(self):
"""Test blocked reactions analysis.
A Pulp solver must be loaded for this test to complete.
Otherwise this test will be skipped.
"""
user_defined_export_rxns_Sji = {
'EX_glc': {
'C00031': -1.0
},
'EX_nad': {
'C00003': -1.0
},
'EX_adp': {
'C00008': -1.0
},
'EX_phosphate': {
'C00009': -1.0
},
'EX_pyruvate': {
'C00022': -1.0
},
'EX_nadh': {
'C00004': -1.0
},
'EX_atp': {
'C00002': -1.0
},
'EX_h2o': {
'C00001': -1.0
},
'EX_hplus': {
'C00080': -1.0
},
'EX_nadp': {
'C00006': -1.0
},
'EX_nadph': {
'C00005': -1.0
}
}
db = load_base_reaction_db(
user_defined_export_rxns_Sji=user_defined_export_rxns_Sji)
custom_flux_constraints = [{
'constraint_name': 'nadphcons1',
'reactions': ['EX_nadph', 'EX_nadh'],
'UB': 2,
'LB': 2
}, {
'constraint_name': 'nadphcons2',
'reactions': ['EX_nadp', 'EX_nad'],
'UB': -2,
'LB': -2
}, {
'constraint_name': 'nadphcons3',
'reactions': ['EX_nadh', 'EX_nad'],
'UB': 0,
'LB': 0
}, {
'constraint_name': 'nadphcons4',
'reactions': ['EX_nadph', 'EX_nadp'],
'UB': 0,
'LB': 0
}]
specific_bounds = {
'EX_glc': {
'LB': -1,
'UB': -1
},
'EX_pyruvate': {
'LB': 2,
'UB': 2
},
'EX_nad': {
'LB': -2,
'UB': 0
},
'EX_nadh': {
'LB': 0,
'UB': 2
},
'EX_nadp': {
'LB': -2,
'UB': 0
},
'EX_nadph': {
'LB': 0,
'UB': 2
},
'EX_adp': {
'LB': -5,
'UB': -1
}, # range 1-5 ATP
'EX_phosphate': {
'LB': -5,
'UB': -1
},
'EX_atp': {
'LB': 1,
'UB': 5
}, # range 1-5 ATP
'EX_h2o': {
'LB': 1,
'UB': 5
},
'EX_hplus': {
'LB': -10,
'UB': 10
}
} # pulp/gurobi has issue with "h+"
pulp_solver = load_pulp_solver(solver_names=ORDERED_SOLVERS,
logger=None)
if not pulp_solver:
self.skipTest(
"Solver is not found. Please install at least one solver.")
exclude_reactions = load_custom_reactions_to_be_excluded()
blocked_reactions_list, FVA_res = blocked_reactions_analysis(
database=db,
pulp_solver=pulp_solver,
specific_bounds=specific_bounds,
custom_flux_constraints=custom_flux_constraints,
excluded_reactions=exclude_reactions,
target_reactions_list=['R01266', 'R07882', 'R00658', 'R01059'])
self.assertEqual(set(blocked_reactions_list), set(['R01266',
'R07882']))