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) == 4)
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_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 test_set_context():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(pa.model.parameters['MAP2K1_0'].value == pa.default_initial_amount)
assert(pa.model.parameters['MAPK3_0'].value == pa.default_initial_amount)
pa.set_context('A375_SKIN')
assert(pa.model.parameters['MAP2K1_0'].value > 10000)
assert(pa.model.parameters['MAPK3_0'].value > 10000)
def test_set_context_monomer_notfound():
st = Phosphorylation(Agent('MAP2K1'), Agent('XYZ'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(pa.model.parameters['MAP2K1_0'].value < 1000)
assert(pa.model.parameters['XYZ_0'].value < 1000)
pa.set_context('A375_SKIN')
assert(pa.model.parameters['MAP2K1_0'].value > 10000)
assert(pa.model.parameters['XYZ_0'].value < 1000)
def test_pysb_assembler_twostep_mixed():
member1 = Agent('BRAF')
member2 = Agent('RAF1')
st1 = Complex([member1, member2])
st2 = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st1, st2])
pa.make_model(policies='two_step')
assert(len(pa.model.rules)==5)
assert(len(pa.model.monomers)==4)
def test_pysb_assembler_phos_twostep_local_to_global():
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')
# This call should have reverted to default policy
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
def test_export_model():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
exp_str = pa.export_model('kappa')
assert(exp_str)
exp_str = pa.export_model('bngl')
assert(exp_str)
exp_str = pa.export_model('sbml', file_name='/dev/null')
assert(exp_str)
def test_mut():
mut = MutCondition('600', 'V', 'E')
st = Phosphorylation(Agent('BRAF', mutations=[mut]), 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.monomer.name == 'BRAF')
assert(braf.site_conditions == {'V600': 'E'})
def test_neg_agent_mod():
mc = ModCondition('phosphorylation', 'serine', '123', False)
st = Phosphorylation(Agent('BRAF', mods=[mc]), Agent('MAP2K2'))
pa = PysbAssembler(policies='one_step')
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.monomer.name == 'BRAF')
assert(braf.site_conditions == {'S123': ('u', WILD)})
def test_translocation():
st = Translocation(Agent('FOXO3A'), 'nucleus', 'cytoplasm')
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(len(pa.model.rules) == 1)
r = pa.model.rules[0]
f1 = r.reactant_pattern.complex_patterns[0].monomer_patterns[0]
assert(f1.site_conditions == {'loc': 'nucleus'})
f2 = r.product_pattern.complex_patterns[0].monomer_patterns[0]
assert(f2.site_conditions == {'loc': 'cytoplasm'})
assert(r.rate_forward.name == 'kf_foxo3a_nucleus_cytoplasm_1')
def test_translocation_loc_special_char():
st = Translocation(Agent('KSR1'), 'cytoplasm', 'cell surface')
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(len(pa.model.rules) == 1)
r = pa.model.rules[0]
f1 = r.reactant_pattern.complex_patterns[0].monomer_patterns[0]
assert(f1.site_conditions == {'loc': 'cytoplasm'})
f2 = r.product_pattern.complex_patterns[0].monomer_patterns[0]
assert(f2.site_conditions == {'loc': 'cell_surface'})
assert(r.rate_forward.name == 'kf_ksr1_cytoplasm_cell_surface_1')
def test_activation_subj1():
"""No subject activity is defined."""
st = Activation(Agent('a'), Agent('b'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
assert(pa.model.monomers['a'].sites == [])
left = pa.model.rules[0].reactant_pattern
subj_left = left.complex_patterns[0].monomer_patterns[0]
right = pa.model.rules[0].product_pattern
subj_right = right.complex_patterns[0].monomer_patterns[0]
assert(subj_left.site_conditions == {})
assert(subj_right.site_conditions == {})
def test_activation_subj3():
"""Subject activity is defined implicitly by another statement."""
st = Activation(Agent('a'), Agent('b'))
st2 = Activation(Agent('c'), Agent('a'))
pa = PysbAssembler()
pa.add_statements([st, st2])
pa.make_model()
assert(pa.model.monomers['a'].sites == ['activity'])
left = pa.model.rules[0].reactant_pattern
subj_left = left.complex_patterns[0].monomer_patterns[0]
right = pa.model.rules[0].product_pattern
subj_right = right.complex_patterns[0].monomer_patterns[0]
assert(subj_left.site_conditions == {u'activity': (u'active')})
assert(subj_right.site_conditions == {u'activity': (u'active')})
def test_activation_subj2():
"""Subject activity is defined explicitly."""
st = Activation(Agent('a'), Agent('b'))
st2 = ActiveForm(Agent('a', mods=[ModCondition('phosphorylation')]),
'activity', True)
pa = PysbAssembler()
pa.add_statements([st, st2])
pa.make_model()
assert(pa.model.monomers['a'].sites == ['phospho'])
left = pa.model.rules[0].reactant_pattern
subj_left = left.complex_patterns[0].monomer_patterns[0]
right = pa.model.rules[0].product_pattern
subj_right = right.complex_patterns[0].monomer_patterns[0]
assert(subj_left.site_conditions == {u'phospho': (u'p', WILD)})
assert(subj_right.site_conditions == {u'phospho': (u'p', WILD)})
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_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_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_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_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_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_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_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_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_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_rasgap1():
gap = Agent('NF1')
ras = Agent('HRAS')
stmt = RasGap(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_rasgef1():
gef = Agent('SOS1')
ras = Agent('HRAS')
stmt = RasGef(gef, 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_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_complex_multiway():
member1 = Agent('BRAF')
member2 = Agent('MEK1')
member3 = Agent('ERK1')
stmt = Complex([member1, member2, member3])
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model(policies='multi_way')
assert (len(model.rules) == 2)
assert (len(model.monomers) == 3)
def test_increaseamount_one_step():
subj = Agent('KRAS')
obj = Agent('BRAF')
st1 = IncreaseAmount(subj, obj)
st2 = IncreaseAmount(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_pysb_assembler_dephos2():
phos = Agent('PP2A')
raf1 = Agent('RAF1')
sub = Agent('MEK1', bound_conditions=[BoundCondition(raf1, True)])
stmt = Dephosphorylation(phos, sub, 'serine', '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_act1():
egfr = Agent('EGFR')
subj = Agent('GRB2', bound_conditions=[BoundCondition(egfr, True)])
obj = Agent('SOS1')
stmt = Activation(subj, obj)
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert (len(model.rules) == 1)
assert (len(model.monomers) == 3)
def test_pysb_assembler_phos2():
hras = Agent('HRAS')
enz = Agent('BRAF', bound_conditions=[BoundCondition(hras, True)])
sub = Agent('MEK1')
stmt = Phosphorylation(enz, sub, 'serine', '222')
pa = PysbAssembler()
pa.add_statements([stmt])
model = pa.make_model()
assert (len(model.rules) == 1)
assert (len(model.monomers) == 3)
def test_decreaseamount_interactions_only():
subj = Agent('KRAS')
obj = Agent('BRAF')
st1 = DecreaseAmount(subj, obj)
st2 = DecreaseAmount(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)
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()
assert (len(model.rules) == 2)
assert (len(model.monomers) == 3)
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_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_unspecified_statement_policies():
enz = Agent('BRAF')
sub = Agent('MEK1')
phos = Agent('PP2A')
stmt1 = Phosphorylation(enz, sub, 'serine', '222')
stmt2 = Dephosphorylation(phos, sub, 'serine', '222')
policies = {'Phosphorylation': 'two_step', 'other': 'interactions_only'}
pa = PysbAssembler(policies=policies)
pa.add_statements([stmt1, stmt2])
model = pa.make_model()
assert (len(model.rules) == 4)
assert (len(model.monomers) == 3)
def check_rule_annotation(stmt, policy):
pa = PysbAssembler(policies=policy)
pa.add_statements([stmt])
model = pa.make_model()
subj = [ann.object for ann in model.annotations
if ann.predicate == 'rule_has_subject']
obj = [ann.object for ann in model.annotations
if ann.predicate == 'rule_has_object']
assert len(subj) == 1
assert subj[0] == 'A'
assert len(obj) == 1
assert obj[0] == 'B'
def test_assemble_export_sbgn():
# Add various statements to test their assembly
st = Phosphorylation(Agent('BRAF'), Agent('MAP2K1'))
mc = ModCondition('phosphorylation', None, None, True)
st2 = Activation(Agent('MAP2K1', mods=[mc]), Agent('MAPK1'))
st3 = Complex([Agent('MAPK1'), Agent('DUSP6')])
st4 = DecreaseAmount(None, Agent('DUSP6'))
pa = PysbAssembler()
pa.add_statements([st, st2, st3, st4])
pa.make_model()
# Export to SBGN
model = pa.export_model('sbgn')
assert model is not None
# Test that the right elements are there in the result
et = ET.fromstring(model)
sbgn_ns = {'s': 'http://sbgn.org/libsbgn/pd/0.1'}
glyphs = et.findall('s:map/s:glyph', namespaces=sbgn_ns)
glyph_classes = [g.attrib.get('class') for g in glyphs]
assert glyph_classes.count('macromolecule') == 6
assert glyph_classes.count('complex') == 2
assert glyph_classes.count('process') == 10
return pa
def _check_mod_assembly(mod_class):
subj = Agent('KRAS')
obj = Agent('BRAF')
st1 = mod_class(subj, obj)
pa = PysbAssembler(policies='interactions_only')
pa.add_statements([st1])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
pa = PysbAssembler(policies='one_step')
pa.add_statements([st1])
model = pa.make_model()
assert(len(model.rules)==1)
assert(len(model.monomers)==2)
pa = PysbAssembler(policies='two_step')
pa.add_statements([st1])
model = pa.make_model()
assert(len(model.rules)==3)
assert(len(model.monomers)==2)
def test_pysb_assembler_actmod2():
mek = Agent('MEK', activity=ActivityCondition('activity', True))
erk = Agent('ERK')
stmts = []
stmts.append(
ActiveForm(
Agent('MEK',
mods=[ModCondition('phosphorylation', 'serine', '218')]),
'activity', True))
stmts.append(
ActiveForm(
Agent('MEK',
mods=[ModCondition('phosphorylation', 'serine', '222')]),
'activity', True))
stmts.append(Phosphorylation(mek, erk, 'threonine', '185'))
stmts.append(Phosphorylation(mek, erk, 'tyrosine', '187'))
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model()
assert (len(model.rules) == 4)
assert (len(model.monomers) == 2)
model = pa.make_model(policies='two_step')
assert (len(model.rules) == 9)
def test_pysb_assembler_actmod1():
mek = Agent('MEK')
erk = Agent('ERK')
stmts = []
mc1 = ModCondition('phosphorylation', 'serine', '218')
mc2 = ModCondition('phosphorylation', 'serine', '222')
stmts.append(ActiveForm(Agent('MEK', mods=[mc1, mc2]), 'activity', True))
stmts.append(Phosphorylation(mek, erk, 'threonine', '185'))
stmts.append(Phosphorylation(mek, erk, 'tyrosine', '187'))
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model()
assert (len(model.rules) == 2)
assert (len(model.monomers) == 2)
def test_non_python_name_bind():
st = Complex([Agent('14-3-3'), Agent('BRAF kinase')])
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
bng.generate_equations(pa.model)
def test_generate_equations():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
bng.generate_equations(pa.model)
def test_save_rst():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
pa.save_rst('/dev/null')
def test_set_context_celltype_notfound():
st = Phosphorylation(Agent('MAP2K1'), Agent('MAPK3'))
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model()
pa.set_context('XYZ')
def test_phos_atpdep():
st = Phosphorylation(Agent('BRAF'), Agent('MEK'), 'S', '222')
pa = PysbAssembler()
pa.add_statements([st])
pa.make_model(policies='atp_dependent')
assert(len(pa.model.rules) == 5)
def test_deubiq_michaelis_menten():
stmt = Deubiquitination(Agent('MEK'), Agent('ERK'))
pa = PysbAssembler()
pa.add_statements([stmt])
pa.make_model(policies='michaelis_menten')
assert(len(pa.model.parameters) == 4)
