def test_increaseamount_hill():
stmt = IncreaseAmount(Agent('TP53'), Agent('MDM2'))
pa = PysbAssembler()
pa.add_statements([stmt])
pa.make_model(policies='hill')
pa.save_model()
assert(len(pa.model.parameters) == 5)
def make_model(text):
"""Given text, return an INDRA model."""
from indra.assemblers import PysbAssembler
pa = PysbAssembler()
pa.add_statements(make_statements(text))
model = pa.make_model(policies='two_step')
return model
def replace_agent(self, agent_name, agent_replacement_names, model_id):
"""Replace an agent in a model with other agents.
This is used, for instance, to expand a protein family to
multiple specific proteins.
"""
for stmt in self.statements[model_id - 1]:
agent_key = [
i for i, m in enumerate(stmt.agent_list())
if m is not None and m.name == agent_name
]
if agent_key:
self.statements[model_id - 1].remove(stmt)
for p in agent_replacement_names:
s = copy.deepcopy(stmt)
if isinstance(stmt, Complex):
s.members[agent_key[0]].name = p
else:
s.__dict__[agent_key[0]].name = p
self.extend_statements([s], model_id)
pa = PysbAssembler()
pa.add_statements(self.statements[model_id - 1])
model = pa.make_model()
pa.add_default_initial_conditions(self.default_initial_amount)
return model
def test_act_michaelis_menten():
stmt = Activation(Agent('MEK'), Agent('ERK'))
stmt2 = Inhibition(Agent('DUSP'), Agent('ERK'))
pa = PysbAssembler()
pa.add_statements([stmt, stmt2])
pa.make_model(policies='michaelis_menten')
assert(len(pa.model.parameters) == 7)
def assemble_model(stmts):
pa = PysbAssembler(policies='one_step')
pa.add_statements(stmts)
model = pa.make_model()
pa.add_default_initial_conditions(100.0)
try:
targeted_agents = get_targeted_agents(stmts)
no_upstream_active_agents = get_no_upstream_active_agents(stmts)
except:
targeted_agents = []
no_upstream_active_agents = []
try:
chemical_agents = get_chemical_agents(stmts)
except:
chemical_agents = []
for m in model.monomers:
try:
if m.name in targeted_agents or m.name in no_upstream_active_agents:
pysb_assembler.set_base_initial_condition(model,
model.monomers[m.name], 50.0)
pysb_assembler.set_extended_initial_condition(model, m, 50.0)
elif m.name in chemical_agents:
pysb_assembler.set_base_initial_condition(model,
model.monomers[m.name], 10000.0)
else:
pysb_assembler.set_extended_initial_condition(model, m, 0)
except:
pysb_assembler.set_extended_initial_condition(model, m, 0)
# Tweak parameters
for param in model.parameters:
if 'kf' in param.name and 'bind' in param.name:
param.value = param.value * 100
return model
def test_annotation():
st = Phosphorylation(Agent('BRAF', db_refs = {'UP': 'P15056'}),
Agent('MAP2K2', db_refs = {'HGNC': '6842'}))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(len(pa.model.annotations) == 5)
def assemble_pysb(stmts, data_genes, out_file):
"""Return an assembled PySB model."""
base_file, _ = os.path.splitext(out_file)
#stmts = ac.load_statements('%s.pkl' % base_file)
stmts = preprocess_stmts(stmts, data_genes)
# This is the "final" set of statements going into the assembler so it
# makes sense to cache these.
# This is also the point where index cards can be generated
ac.dump_statements(stmts, '%s_before_pa.pkl' % base_file)
assemble_index_cards(stmts, 'output/index_cards')
# Save a version of statements with no evidence for faster loading
for s in stmts:
s.evidence = []
for ss in s.supports + s.supported_by:
ss.evidence = []
ac.dump_statements(stmts, '%s_no_evidence.pkl' % base_file)
# Assemble model
pa = PysbAssembler()
pa.add_statements(stmts)
pa.make_model(reverse_effects=False)
#ac.dump_statements(pa.statements, '%s_after_pa.pkl' % base_file)
# Set context
set_context(pa)
# Add observables
add_observables(pa.model)
pa.save_model(out_file)
with open('korkut_pysb.pkl', 'wb') as fh:
pickle.dump(pa.model, fh)
#pa.export_model('kappa', '%s.ka' % base_file)
return pa.model
def test_missing_catalytic_default_site():
c8 = Agent('CASP8', activity=ActivityCondition('catalytic', True))
c3 = Agent('CASP3')
stmt = Activation(c8, c3, 'catalytic')
# Interactions only
pa = PysbAssembler(policies='interactions_only')
pa.add_statements([stmt])
model = pa.make_model()
# One step
pa = PysbAssembler(policies='one_step')
pa.add_statements([stmt])
model = pa.make_model()
# Two step
pa = PysbAssembler(policies='two_step')
pa.add_statements([stmt])
model = pa.make_model()
def test_missing_transcription_default_site():
p53 = Agent('TP53', activity=ActivityCondition('transcription', True))
bax = Agent('BAX')
stmt = Activation(p53, bax)
# Interactions only
pa = PysbAssembler(policies='interactions_only')
pa.add_statements([stmt])
model = pa.make_model()
# One step
pa = PysbAssembler(policies='one_step')
pa.add_statements([stmt])
model = pa.make_model()
# Two step
pa = PysbAssembler(policies='two_step')
pa.add_statements([stmt])
model = pa.make_model()
def test_pysb_assembler_autophos1():
enz = Agent('MEK1')
stmt = Autophosphorylation(enz, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==1)
def test_convert_subj():
stmt = Conversion(Agent('PIK3CA'), [Agent('PIP2')], [Agent('PIP3')])
pa = PysbAssembler()
pa.add_statements([stmt])
pa.make_model()
assert(len(pa.model.parameters) == 4)
assert(len(pa.model.rules) == 1)
assert(len(pa.model.monomers) == 3)
def get_model_checker(statements):
pa = PysbAssembler()
pa.add_statements(statements)
model = pa.make_model()
stmt = Influence(Concept('crop_production'), Concept('food_security'))
mc = ModelChecker(model, [stmt])
mc.prune_influence_map()
return mc
def test_pysb_assembler_actsub():
stmt = ActiveForm(Agent('BRAF', mutations=[MutCondition('600', 'V', 'E')]),
'activity', True)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model(policies='two_step')
assert(len(model.rules)==0)
assert(len(model.monomers)==1)
def test_pysb_assembler_gef1():
gef = Agent('SOS1')
ras = Agent('HRAS')
stmt = Gef(gef, ras)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_non_python_name_phos():
st = Phosphorylation(Agent('14-3-3'), Agent('BRAF kinase'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
names = [m.name for m in pa.model.monomers]
assert('BRAF_kinase' in names)
assert('p14_3_3' in names)
bng.generate_equations(pa.model)
def test_annotation_regamount():
st1 = IncreaseAmount(Agent('BRAF', db_refs = {'UP': 'P15056'}),
Agent('MAP2K2', db_refs = {'HGNC': '6842'}))
st2 = DecreaseAmount(Agent('BRAF', db_refs = {'UP': 'P15056'}),
Agent('MAP2K2', db_refs = {'HGNC': '6842'}))
pa = PysbAssembler()
pa.add_statements([st1, st2])
pa.make_model()
assert(len(pa.model.annotations) == 8)
def test_agent_loc():
st = Phosphorylation(Agent('BRAF', location='cytoplasm'), Agent('MEK'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(len(pa.model.rules) == 1)
r = pa.model.rules[0]
braf = r.reactant_pattern.complex_patterns[0].monomer_patterns[0]
assert(braf.site_conditions == {'loc': 'cytoplasm'})
def assemble_model(model_indra_str):
stmts = decode_indra_stmts(model_indra_str)
pa = PysbAssembler(policies='two_step')
pa.add_statements(stmts)
model = pa.make_model()
pa.add_default_initial_conditions(100.0)
for m in model.monomers:
pysb_assembler.set_extended_initial_condition(model, m, 0)
return model
def test_activity_activity3():
subj = Agent('Vemurafenib')
obj = Agent('BRAF')
stmt = Inhibition(subj, obj)
pa = PysbAssembler(policies='one_step')
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_pysb_assembler_complex_twostep():
member1 = Agent('BRAF')
member2 = Agent('MEK1')
stmt = Complex([member1, member2])
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model(policies='two_step')
assert(len(model.rules)==2)
assert(len(model.monomers)==2)
def test_activity_activity():
subj = Agent('KRAS')
obj = Agent('BRAF')
stmt = Activation(subj, obj)
pa = PysbAssembler(policies='interactions_only')
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_pysb_assembler_autophos2():
raf1 = Agent('RAF1')
enz = Agent('MEK1', bound_conditions=[BoundCondition(raf1, True)])
stmt = Autophosphorylation(enz, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_pysb_assembler_phos_twostep_local():
enz = Agent('BRAF')
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model(policies='two_step')
assert(len(model.rules)==3)
assert(len(model.monomers)==2)
def test_pysb_assembler_gap1():
gap = Agent('NF1')
ras = Agent('HRAS')
stmt = Gap(gap, ras)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_pysb_assembler_transphos1():
egfr = Agent('EGFR')
enz = Agent('EGFR', bound_conditions=[BoundCondition(egfr, True)])
stmt = Transphosphorylation(enz, 'tyrosine')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==1)
def test_pysb_assembler_dephos_twostep1():
phos = Agent('PP2A')
sub = Agent('MEK1')
stmt = Dephosphorylation(phos, sub, 'serine', '222')
pa = PysbAssembler(policies='two_step')
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==3)
assert(len(model.monomers)==2)
def test_pysb_assembler_dephos_noenz():
enz = None
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==0)
assert(len(model.monomers)==0)
def test_activeform_site():
a = Agent('A', db_refs={'HGNC': '1234'})
b = Agent('B', db_refs={'HGNC': '5678'})
b_phos = Agent('B', mods=[ModCondition('phosphorylation', 'Y', '200')],
db_refs={'HGNC': '5678'})
st1 = Phosphorylation(a, b, 'S', '100')
st2 = ActiveForm(b_phos, 'kinase', True)
pa = PysbAssembler(policies='one_step')
pa.add_statements([st1, st2])
model = pa.make_model()
def test_decreaseamount_one_step():
subj = Agent('KRAS')
obj = Agent('BRAF')
st1 = DecreaseAmount(subj, obj)
st2 = DecreaseAmount(None, obj)
pa = PysbAssembler(policies='one_step')
pa.add_statements([st1, st2])
model = pa.make_model()
assert(len(model.rules)==2)
assert(len(model.monomers)==2)
def test_increaseamount_interactions_only():
subj = Agent('KRAS')
obj = Agent('BRAF')
st1 = IncreaseAmount(subj, obj)
st2 = IncreaseAmount(None, obj)
pa = PysbAssembler(policies='interactions_only')
pa.add_statements([st1, st2])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
