def test_solve(self):
"""Test the complete linear programing solution, using the
example from the documentation"""
mat = [
[ 1.0, 1.0, 1.0],
[10.0, 4.0, 5.0],
[ 2.0, 2.0, 6.0],
]
lp.load(mat)
lp.objective_coefficients([ 10.0, 6.0, 4.0 ])
lp.row_bounds([(None, 100.0), (None, 600.0), (None, 300.0)])
lp.col_bounds([(0, None), (0, None), (0, None)])
status, result = lp.solve()
r = "%0.3f" % result
self.assertEqual(r, "733.333")
self.assertEqual(status, 'opt')
def test_primals(self):
"""Test getting the primals back as a list"""
mat = [
[ 1.0, 1.0, 1.0],
[10.0, 4.0, 5.0],
[ 2.0, 2.0, 6.0],
]
rh = ['a', 'b', 'c']
ch = ['x', 'y', 'z']
lp.load(mat, rh, ch)
lp.objective_coefficients([ 10.0, 6.0, 4.0 ])
lp.row_bounds([(None, 100.0), (None, 600.0), (None, 300.0)])
lp.col_bounds([(0, None), (0, None), (0, None)])
status, result = lp.solve()
col_pri = [33.333333333333336, 66.66666666666666, 0.0]
col_res = lp.col_primals()
self.assertEqual(col_pri, col_res)
parser.add_argument('-m', '--media', help="Media input file")
parser.add_argument('-o', '--out', help="Output file")
parser.add_argument('-v',
'--verbose',
action="store_true",
help="Output status messages")
args = parser.parse_args()
sbmlf = args.sbml
output = args.out if args.out else None
mediaf = args.media if args.media else None
verbose = args.verbose
doc = parse_sbml_file(sbmlf)
model = doc.getModel()
if mediaf:
media = parse_media_file(mediaf)
else:
media = None
compound_ids, reaction_ids, stiochio_m, objFunc = parse_stoichiometry(
model)
compound_ids, reaction_ids = create_smatrix(compound_ids, reaction_ids,
stiochio_m, objFunc)
reaction_bounds(model, reaction_ids, media)
compound_bounds(compound_ids)
status, value = lp.solve()
print("Solved the FBA with status: {}".format(status))
print("Objective value: {}".format(value))
if __name__ == '__main__':
parser = argparse.ArgumentParser()
parser.add_argument("sbml", help='SBML Model file')
parser.add_argument('-m', '--media', help="Media input file")
parser.add_argument('-o', '--out', help="Output file")
parser.add_argument('-v', '--verbose', action="store_true",
help="Output status messages")
args = parser.parse_args()
sbmlf = args.sbml
output = args.out if args.out else None
mediaf = args.media if args.media else None
verbose = args.verbose
doc = parse_sbml_file(sbmlf)
model = doc.getModel()
if mediaf:
media = parse_media_file(mediaf)
else:
media = None
cpdIds, rxnIds, sm, objFunc = parse_stoichiometry(model)
cpdIds, rxnIds = createSMatrix(cpdIds, rxnIds, sm, objFunc)
reaction_bounds(model, rxnIds, media)
compound_bounds(cpdIds)
status, value = lp.solve()
print("Solved the FBA with status: {}".format(status))
print("Objective value: {}".format(value))