def test_long_string_model(self):
long_string = '''---
name: Test model
biomass: rxn_1
reactions:
- id: rxn_1
equation: '|A_\u2206[e]| => |B[c]|'
genes:
- gene_1
- gene_2
- id: rxn_2_\u03c0
equation: '|B[c]| => |C[e]|'
genes: 'gene_3 or (gene_4 and gene_5)'
compounds:
- id: A_\u2206
- id: B
- id: C
exchange:
- compartment: e
compounds:
- id: A_\u2206
- id: C
limits:
- reaction: rxn_2_\u03c0
upper: 100
'''
m = native.ModelReader(long_string)
self.assertEqual(m.name, 'Test model')
self.assertEqual(m.biomass_reaction, 'rxn_1')
self.assertEqual(m.extracellular_compartment, 'e')
reactions = list(m.parse_reactions())
self.assertEqual(reactions[0].id, 'rxn_1')
def test_long_string_model_include(self):
longString = '''---
name: Test model
biomass: rxn_1
reactions:
- include: exchange.yaml
'''
m = native.ModelReader(longString)
with self.assertRaises(context.ContextError):
list(m.parse_reactions())
def setUp(self):
reader = native.ModelReader({
'compartments': [{
'id': 'c',
'adjacent_to': 'e'
}, {
'id': 'e'
}],
'reactions': [{
'id': 'rxn_1',
'equation': 'A[e] <=> B[c]'
}, {
'id': 'rxn_2',
'equation': 'A[e] => C[c]'
}, {
'id': 'rxn_3',
'equation': 'A[e] => D[e]'
}, {
'id': 'rxn_4',
'equation': 'C[c] => D[e]'
}],
'compounds': [{
'id': 'A'
}, {
'id': 'B'
}, {
'id': 'C'
}, {
'id': 'D'
}],
'exchange': [{
'compartment':
'e',
'compounds': [{
'id': 'A',
'reaction': 'rxn_5'
}, {
'id': 'D',
'reaction': 'rxn_6'
}]
}],
'model': [{
'reactions': ['rxn_1', 'rxn_2']
}]
})
self._model = reader.create_model()
def test_dict_model(self):
dict_model = {
'name':
'Test model',
'biomass':
'rxn_1',
'reactions': [{
'id': 'rxn_1',
'equation': '|A_\u2206[e]| => |B[c]|',
'genes': ['gene_1', 'gene_2']
}, {
'id': 'rxn_2_\u03c0',
'equation': '|B[c]| => |C[e]|',
'genes': 'gene_3 or (gene_4 and gene_5)'
}],
'compounds': [{
'id': 'A_\u2206'
}, {
'id': 'B'
}, {
'id': 'C'
}],
'exchange': [{
'compartment': 'e',
'compounds': [{
'id': 'A_\u2206'
}, {
'id': 'C'
}]
}],
'limits': [{
'reaction': 'rxn_2_\u03c0',
'upper': 100
}]
}
dmodel = native.ModelReader(dict_model)
self.assertEqual(dmodel.name, 'Test model')
self.assertEqual(dmodel.biomass_reaction, 'rxn_1')
self.assertEqual(dmodel.extracellular_compartment, 'e')
def test_parse_compartments(self):
model_dict = {
'compartments': [{
'id': 'e',
'name': 'Extracellular'
}, {
'id': 'p',
'name': 'Periplasm',
'adjacent_to': ['e', 'c']
}, {
'id': 'c',
'name': 'Cytosol',
'adjacent_to': 'p'
}, {
'id': 'internal',
'name': 'Internal compartment',
'adjacent_to': 'c'
}]
}
reader = native.ModelReader(model_dict)
compartment_iter, boundaries = reader.parse_compartments()
compartments = list(compartment_iter)
self.assertEqual(len(compartments), 4)
self.assertEqual(compartments[0].id, 'e')
self.assertEqual(compartments[0].name, 'Extracellular')
self.assertEqual(compartments[1].id, 'p')
self.assertEqual(compartments[1].name, 'Periplasm')
self.assertEqual(compartments[2].id, 'c')
self.assertEqual(compartments[2].name, 'Cytosol')
self.assertEqual(compartments[3].id, 'internal')
self.assertEqual(compartments[3].name, 'Internal compartment')
normalized_boundaries = set(
tuple(sorted((c1, c2))) for c1, c2 in boundaries)
self.assertSetEqual(normalized_boundaries, {('c', 'internal'),
('c', 'p'), ('e', 'p')})
def test_invalid_model_type(self):
with self.assertRaises(ValueError):
native.ModelReader(42.2)
def setUp(self):
reader = native.ModelReader({
'name':
'Test model',
'biomass':
'rxn_1',
'compartments': [{
'id': 'e',
'name': 'Extracellular',
'adjacent_to': ['c']
}, {
'id': 'c',
'name': 'Cytosol',
'adjacent_to': 'e'
}],
'reactions': [{
'id': 'rxn_1',
'name': 'Reaction 1',
'equation': '|A_\u2206[e]| => |B[c]|',
'genes': ['gene_1', 'gene_2']
}, {
'id': 'rxn_2_\u03c0',
'name': 'Reaction 2',
'equation': 'atp[c] + (2) |B[c]| <=> adp[c] + |C[e]|',
'genes': 'gene_3 or (gene_4 and gene_5)'
}, {
'id': 'rxn_3',
'equation': 'D[c] => E[c]'
}],
'compounds': [{
'id': 'A_\u2206',
'name': 'Compound A',
'charge': 0
}, {
'id': 'B',
'name': 'Compound B',
'formula': 'H2O',
'charge': -1
}, {
'id': 'C',
'charge': -1,
'formula': 'O2'
}, {
'id': 'atp',
'name': '\u2192 ATP ',
'charge': -4,
'formula': 'C10H12N5O13P3'
}, {
'id': 'adp',
'name': ' ADP',
'charge': -3,
'formula': 'C10H12N5O10P2'
}],
'exchange': [{
'compartment': 'e',
'compounds': [{
'id': 'A_\u2206'
}, {
'id': 'C'
}]
}],
'limits': [{
'reaction': 'rxn_2_\u03c0',
'upper': 100
}]
})
self._model = reader.create_model()
reader = native.ModelReader({
'biomass':
'rxn_1',
'reactions': [{
'id': 'rxn_1',
'equation': 'A[c] => B[c]'
}],
'limits': [{
'reaction': 'rxn_1',
'fixed': 10
}]
})
self._infeasible_model = reader.create_model()