def make_model(text):
"""Given text, return an INDRA model."""
from indra.pysb_assembler import PysbAssembler
pa = PysbAssembler()
pa.add_statements(make_statements(text))
model = pa.make_model(policies='two_step')
return model
def test_trips_processor_offline():
"""Smoke test to see if imports and executes without error. Doesn't
check for correctness of parse or of assembled model."""
pa = PysbAssembler()
tp = trips_api.process_xml(open(test_small_file).read())
pa.add_statements(tp.statements)
model = pa.make_model()
def test_trips_processor_offline():
"""Smoke test to see if imports and executes without error. Doesn't
check for correctness of parse or of assembled model."""
pa = PysbAssembler()
tp = trips_api.process_xml(open(test_small_file).read())
pa.add_statements(tp.statements)
model = pa.make_model()
def test_pysb_assembler_autophos1():
enz = Agent('MEK1')
stmt = Autophosphorylation(enz, 'PhosphorylationSerine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==1)
def test_pysb_assembler_autophos1():
enz = Agent('MEK1')
stmt = Autophosphorylation(enz, 'PhosphorylationSerine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert (len(model.rules) == 1)
assert (len(model.monomers) == 1)
def test_pysb_assembler_complex1():
member1 = Agent('BRAF')
member2 = Agent('MEK1')
stmt = Complex([member1, member2])
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==2)
assert(len(model.monomers)==2)
def test_pysb_assembler_complex1():
member1 = Agent('BRAF')
member2 = Agent('MEK1')
stmt = Complex([member1, member2])
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert (len(model.rules) == 2)
assert (len(model.monomers) == 2)
def test_pysb_assembler_transphos1():
enz = Agent('EGFR', bound_to='EGFR')
stmt = Transphosphorylation(enz, 'PhosphorylationTyrosine', None,
'', '', '', '')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert(len(model.rules)==1)
assert(len(model.monomers)==1)
def test_pysb_assembler_autophos2():
raf1 = Agent('RAF1')
enz = Agent('MEK1', bound_conditions=[BoundCondition(raf1, True)])
stmt = Autophosphorylation(enz, 'PhosphorylationSerine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_pysb_assembler_phos2():
hras = Agent('HRAS')
enz = Agent('BRAF', bound_conditions=[BoundCondition(hras, True)])
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'PhosphorylationSerine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==3)
def test_pysb_assembler_dephos_twostep1():
phos = Agent('PP2A')
sub = Agent('MEK1')
stmt = Dephosphorylation(phos, sub, 'PhosphorylationSerine', '222')
pa = PysbAssembler(policies='two_step')
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert(len(model.rules)==3)
assert(len(model.monomers)==2)
def test_pysb_assembler_rasgap1():
gap = Agent('NF1')
ras = Agent('HRAS')
stmt = RasGap(gap, 'catalytic', ras, '', '', '', '')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
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, 'PhosphorylationTyrosine', None)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert (len(model.rules) == 1)
assert (len(model.monomers) == 1)
def test_pysb_assembler_transphos1():
egfr = Agent('EGFR')
enz = Agent('EGFR', bound_conditions=[BoundCondition(egfr, True)])
stmt = Transphosphorylation(enz, 'PhosphorylationTyrosine', None)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert(len(model.rules)==1)
assert(len(model.monomers)==1)
def test_pysb_assembler_rasgap1():
gap = Agent('NF1')
ras = Agent('HRAS')
stmt = RasGap(gap, 'catalytic', ras)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert (len(model.rules) == 1)
assert (len(model.monomers) == 2)
def test_pysb_assembler_phos4():
enz = Agent('BRAF', bound_to='HRAS')
sub = Agent('MEK1', bound_to='ERK1', bound_neg=True)
stmt = Phosphorylation(enz, sub, 'PhosphorylationSerine', '222',
'', '', '', '')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==4)
def test_pysb_assembler_phos2():
hras = Agent('HRAS')
enz = Agent('BRAF', bound_conditions=[BoundCondition(hras, True)])
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'PhosphorylationSerine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert (len(model.rules) == 1)
assert (len(model.monomers) == 3)
def test_pysb_assembler_autophos2():
raf1 = Agent('RAF1')
enz = Agent('MEK1', bound_conditions=[BoundCondition(raf1, True)])
stmt = Autophosphorylation(enz, 'PhosphorylationSerine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert (len(model.rules) == 1)
assert (len(model.monomers) == 2)
def test_pysb_assembler_dephos_twostep1():
phos = Agent('PP2A')
sub = Agent('MEK1')
stmt = Dephosphorylation(phos, sub, 'PhosphorylationSerine', '222')
pa = PysbAssembler(policies='two_step')
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert (len(model.rules) == 3)
assert (len(model.monomers) == 2)
def test_pysb_assembler_rasgef1():
gef = Agent('SOS1')
ras = Agent('HRAS')
stmt = RasGef(gef, 'catalytic', ras)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_pysb_assembler_dephos2():
phos = Agent('PP2A')
raf1 = Agent('RAF1')
sub = Agent('MEK1', bound_conditions=[BoundCondition(raf1, True)])
stmt = Dephosphorylation(phos, sub, 'PhosphorylationSerine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert (len(model.rules) == 1)
assert (len(model.monomers) == 3)
def test_pysb_assembler_actact1():
egfr = Agent('EGFR')
subj = Agent('GRB2', bound_conditions=[BoundCondition(egfr, True)])
obj = Agent('SOS1')
stmt = ActivityActivity(subj, 'act', 'increase', obj, 'act')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert (len(model.rules) == 1)
assert (len(model.monomers) == 3)
def test_pysb_assembler_actact1():
egfr = Agent('EGFR')
subj = Agent('GRB2', bound_conditions=[BoundCondition(egfr, True)])
obj = Agent('SOS1')
stmt = ActivityActivity(subj, 'act', 'increase', obj, 'act')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert(len(model.rules)==1)
assert(len(model.monomers)==3)
def test_pysb_assembler_complex3():
hras = Agent('HRAS')
member1 = Agent('BRAF', bound_conditions=[BoundCondition(hras, True)])
member2 = Agent('MEK1')
stmt = Complex([member1, member2])
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert (len(model.rules) == 2)
assert (len(model.monomers) == 3)
def test_pysb_assembler_dephos2():
phos = Agent('PP2A')
sub = Agent('MEK1', bound_to='RAF1')
stmt = Dephosphorylation(phos, sub, 'PhosphorylationSerine', '222',
'', '', '', '')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert(len(model.rules)==1)
assert(len(model.monomers)==3)
def test_pysb_assembler_actact1():
subj = Agent('GRB2', bound_to='EGFR')
obj = Agent('SOS1')
stmt = ActivityActivity(subj, 'act', 'increase', obj, 'act',
'', '', '', '')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert(len(model.rules)==1)
assert(len(model.monomers)==3)
def test_pysb_assembler_complex3():
hras = Agent('HRAS')
member1 = Agent('BRAF', bound_conditions=[BoundCondition(hras, True)])
member2 = Agent('MEK1')
stmt = Complex([member1, member2])
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
print model.rules
assert(len(model.rules)==2)
assert(len(model.monomers)==3)
def test_unspecified_statement_policies():
enz = Agent('BRAF')
sub = Agent('MEK1')
phos = Agent('PP2A')
stmt1 = Phosphorylation(enz, sub, 'PhosphorylationSerine', '222')
stmt2 = Dephosphorylation(phos, sub, 'PhosphorylationSerine', '222')
policies = {'Phosphorylation': 'two_step', 'other': 'interactions_only'}
pa = PysbAssembler(policies=policies)
pa.add_statements([stmt1, stmt2])
model = pa.make_model()
print model.rules
assert (len(model.rules) == 4)
assert (len(model.monomers) == 3)
def test_unspecified_statement_policies():
enz = Agent('BRAF')
sub = Agent('MEK1')
phos = Agent('PP2A')
stmt1 = Phosphorylation(enz, sub, 'PhosphorylationSerine', '222')
stmt2 = Dephosphorylation(phos, sub, 'PhosphorylationSerine', '222')
policies = {'Phosphorylation': 'two_step',
'other': 'interactions_only'}
pa = PysbAssembler(policies=policies)
pa.add_statements([stmt1, stmt2])
model = pa.make_model()
print model.rules
assert(len(model.rules)==4)
assert(len(model.monomers)==3)
def test_pysb_assembler_actmod1():
mek = Agent('MEK')
erk = Agent('ERK')
stmts = []
stmts.append(ActivityModification(mek, ['PhosphorylationSerine',
'PhosphorylationSerine'], [218,222],
'increases', 'act'))
stmts.append(Phosphorylation(mek, erk, 'PhosphorylationThreonine', '185'))
stmts.append(Phosphorylation(mek, erk, 'PhosphorylationTyrosine', '187'))
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model()
print model.rules
assert(len(model.rules)==2)
assert(len(model.monomers)==2)
def test_pysb_assembler_actmod1():
mek = Agent('MEK')
erk = Agent('ERK')
stmts = []
stmts.append(
ActivityModification(
mek, ['PhosphorylationSerine', 'PhosphorylationSerine'],
[218, 222], 'increases', 'act'))
stmts.append(Phosphorylation(mek, erk, 'PhosphorylationThreonine', '185'))
stmts.append(Phosphorylation(mek, erk, 'PhosphorylationTyrosine', '187'))
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model()
print model.rules
assert (len(model.rules) == 2)
assert (len(model.monomers) == 2)
def test_hyphenated_agent_names():
"""This query should contain reactions with agent names RAF1-BRAF,
which need to be canonicalized to Python-compatible names before
model assembly."""
bp = biopax_api.process_pc_neighborhood(['BRAF'])
bp.get_phosphorylation()
pa = PysbAssembler()
pa.add_statements(bp.statements)
pa.make_model()
def test_trips_processor_online():
"""Smoke test to see if imports and executes without error. Doesn't
check for correctness of parse or of assembled model."""
pa = PysbAssembler()
tp = trips_api.process_text('BRAF phosphorylates MEK1 at Ser222.')
pa.add_statements(tp.statements)
def test_trips_processor_online():
"""Smoke test to see if imports and executes without error. Doesn't
check for correctness of parse or of assembled model."""
pa = PysbAssembler()
tp = trips_api.process_text('BRAF phosphorylates MEK1 at Ser222.')
pa.add_statements(tp.statements)
