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_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_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_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_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(): 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_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_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_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_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_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_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') 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(): 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_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_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_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)