def test_modification():
st1 = Phosphorylation(Agent('BRAF'), Agent('MAP2K1'), 'S', '222')
sa = SifAssembler([st1])
sa.make_model(True, True, True)
assert len(sa.graph.nodes()) == 2
assert len(sa.graph.edges()) == 1
sa.save_model('test_sif.sif', True)
with open('test_sif.sif', 'rb') as fh:
txt = fh.read().decode('utf-8')
assert txt == 'BRAF 0 MAP2K1\n', txt
bn_str = boolean2.modify_states(bn_str, turnon=on, turnoff=off)
model = boolean2.Model(text=bn_str, mode='async')
for i in range(nsim):
model.initialize()
model.iterate(steps=nsteps)
coll.collect(states=model.states, nodes=model.nodes)
avgs = coll.get_averages(normalize=True)
return avgs
if __name__ == '__main__':
# Build Boolean net for basic pathway
st = ac.load_statements('ras_pathway.pkl')
sa = SifAssembler(st)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway.sif')
bn_str = sa.print_boolean_net('ras_pathway_bn.txt')
# Build Boolean net for extended pathway
st_ext = ac.load_statements('ras_pathway_extension.pkl')
sa = SifAssembler(st + st_ext)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway_extension.sif')
bn_str = sa.print_boolean_net('ras_pathway_extension_bn.txt')
# Condition 1
off = []
on = ['GROWTH-FACTOR']
avgs = get_sim_avgs(bn_str, off=off, on=on)
jun_basic_noinh = avgs['JUN']
bn_str = boolean2.modify_states(bn_str, turnon=on, turnoff=off)
model = boolean2.Model(text=bn_str, mode='async')
for i in range(nsim):
model.initialize()
model.iterate(steps=nsteps)
coll.collect(states=model.states, nodes=model.nodes)
avgs = coll.get_averages(normalize=True)
return avgs
if __name__ == '__main__':
# Build Boolean net for basic pathway
st = ac.load_statements('ras_pathway.pkl')
sa = SifAssembler(st)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway.sif')
bn_str = sa.print_boolean_net('ras_pathway_bn.txt')
# Build Boolean net for extended pathway
st_ext = ac.load_statements('ras_pathway_extension.pkl')
sa = SifAssembler(st + st_ext)
sa.make_model(use_name_as_key=True)
sa.save_model('ras_pathway_extension.sif')
bn_str = sa.print_boolean_net('ras_pathway_extension_bn.txt')
# Condition 1
off = []
on = ['GROWTH-FACTOR']
avgs = get_sim_avgs(bn_str, off=off, on=on)
jun_basic_noinh = avgs['JUN']