def test_merge(self):
model = native.NativeModel()
model.compounds.update([
entry.DictCompoundEntry({
'id': 'g6p_c',
'name': 'G6P'
}),
entry.DictCompoundEntry({
'id': 'g6p_e',
'name': 'G6P'
})
])
model.reactions.update([
entry.DictReactionEntry({
'id':
'TP_g6p',
'equation':
parse_reaction('g6p_c[c] <=> g6p_e[e]')
})
])
exchange_compound = Compound('g6p_e', 'e')
model.exchange[exchange_compound] = (exchange_compound, 'EX_g6p_e',
-10, 0)
sbml.merge_equivalent_compounds(model)
self.assertEqual({entry.id for entry in model.compounds}, {'g6p'})
self.assertEqual(model.reactions['TP_g6p'].equation,
parse_reaction('g6p[c] <=> g6p[e]'))
new_exchange_compound = Compound('g6p', 'e')
self.assertEqual(model.exchange[new_exchange_compound],
(new_exchange_compound, 'EX_g6p_e', -10, 0))
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
media:
- compartment: e
compounds:
- id: A_\u2206
- id: C
limits:
- reaction: rxn_2_\u03c0
upper: 100
'''
m = native.NativeModel(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 setUp(self):
self.model = native.NativeModel()
self.model.reactions.update([
entry.DictReactionEntry({
'id': 'EX_g6p',
'equation': parse_reaction('g6p[e] <=>')
}),
entry.DictReactionEntry({
'id': 'EX_glc-D',
'equation': parse_reaction('glc-D[e] <=>')
}),
entry.DictReactionEntry({
'id': 'SINK_glc-D',
'equation': parse_reaction('glc-D[c] <=>')
}),
entry.DictReactionEntry({
'id':
'rxn_1',
'equation':
parse_reaction('g6p[c] <=> glc-D[c]')
}),
entry.DictReactionEntry({
'id':
'TP_glc-D',
'equation':
parse_reaction('glc-D[c] <=> glc-D[e]')
})
])
def test_long_string_model_include(self):
longString = '''---
name: Test model
biomass: rxn_1
reactions:
- include: medium.yaml
'''
m = native.NativeModel(longString)
with self.assertRaises(context.ContextError):
list(m.parse_reactions())
def test_parse_model_file_with_media(self):
path = self.write_model_file(
'model.yaml', '\n'.join([
'extracellular: Ex', 'media:', ' - compounds:', ' - id: A',
' - id: B', ' compartment: c'
]))
model = native.NativeModel(path)
medium = list(model.parse_medium())
self.assertEqual(medium[0][0], Compound('A', 'Ex'))
self.assertEqual(medium[1][0], Compound('B', 'c'))
def test_parse_model_file(self):
path = self.write_model_file(
'model.yaml', '\n'.join([
'name: Test model', 'biomass: biomass_reaction_id',
'extracellular: Extra', 'default_flux_limit: 500'
]))
model = native.NativeModel(path)
self.assertEqual(model.get_name(), 'Test model')
self.assertEqual(model.get_biomass_reaction(), 'biomass_reaction_id')
self.assertEqual(model.get_extracellular_compartment(), 'Extra')
self.assertEqual(model.get_default_flux_limit(), 500)
def test_properties(self):
model = native.NativeModel()
model.name = 'Test model'
model.version_string = '1.0'
model.biomass_reaction = 'rxn_1'
model.extracellular_compartment = 'e'
model.default_compartment = 'c'
model.default_flux_limit = 1000
self.assertEqual(model.name, 'Test model')
self.assertEqual(model.version_string, '1.0')
self.assertEqual(model.biomass_reaction, 'rxn_1')
self.assertEqual(model.extracellular_compartment, 'e')
self.assertEqual(model.default_compartment, 'c')
self.assertEqual(model.default_flux_limit, 1000)
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'
}],
'media': [{
'compartment': 'e',
'compounds': [{
'id': 'A_\u2206'
}, {
'id': 'C'
}]
}],
'limits': [{
'reaction': 'rxn_2_\u03c0',
'upper': 100
}]
}
dmodel = native.NativeModel(dict_model)
self.assertEqual(dmodel.name, 'Test model')
self.assertEqual(dmodel.biomass_reaction, 'rxn_1')
self.assertEqual(dmodel.extracellular_compartment, 'e')
def test_invalid_model_type(self):
with self.assertRaises(ValueError):
native.NativeModel(42.2)
def _import(self, file, name):
model_doc = loadmat(file)
if name is None:
names = [
k for k in model_doc.keys()
if k not in ['__header__', '__version__', '__globals__']
]
modelnames = list()
for i in names:
if (isinstance(model_doc[i], np.ndarray)
and len(model_doc[i].dtype) > 1):
modelnames.append(i)
if len(modelnames) == 1:
name = str(modelnames[0])
model_doc = model_doc[modelnames[0]]
elif len(modelnames) > 1:
raise ModelLoadError(('More than one model exist, '
'please choose from: %s '
'using --model-name' % modelnames))
else:
raise ModelLoadError('Incorrect format')
else:
if name not in model_doc.keys():
raise ModelLoadError('Incorrect model name specified')
else:
model_doc = model_doc[name]
if not (isinstance(model_doc, np.ndarray)
and len(model_doc.dtype) > 1):
raise ModelLoadError('Incorrect format')
model = native.NativeModel()
model.name = name
self._compartments_from_compound = set()
self._origid_compound = dict()
model.compounds.update(self._read_compounds(model_doc))
model.compartments.update(self._compartments_from_compound)
self._boundary_compartment = None
# Add model level compartment information
if all(var in model_doc.dtype.names for var in ['comps', 'compNames']):
model.compartments.update(self._read_compartments(model_doc))
for comp in model.compartments:
if comp.name.lower() == 'boundary': # has boundary compartment
self._boundary_compartment = comp.id
model.compartments.discard(self._boundary_compartment)
for reaction, lower, upper in self._read_reactions(model_doc):
model.reactions.add_entry(reaction)
if lower is not None and upper is not None:
model.limits[reaction.id] = reaction.id, lower, upper
biomass_reaction = None
objective_reactions = set()
if 'c' in model_doc.dtype.names:
for i in range(len(model_doc['c'][0, 0])):
if model_doc['c'][0, 0][i][0] != 0:
objective_reactions.add(
str(model_doc['rxns'][0, 0][i][0][0]))
if len(objective_reactions) == 1:
biomass_reaction = next(iter(objective_reactions))
logger.info(
'Detected biomass reaction: {}'.format(biomass_reaction))
elif len(objective_reactions) > 1:
logger.warning(
'Multiple reactions are used as the'
' biomass reaction: {}'.format(objective_reactions))
else:
logger.warning('No objective reaction')
model.biomass_reaction = biomass_reaction
return model