def assemble_pysb(stmts, data_genes, out_file):
"""Return an assembled PySB model."""
stmts = ac.filter_direct(stmts)
stmts = ac.filter_belief(stmts, 0.95)
stmts = ac.filter_top_level(stmts)
stmts = ac.filter_gene_list(stmts, data_genes, 'all')
stmts = ac.reduce_activities(stmts)
pa = PysbAssembler()
pa.add_statements(stmts)
model = pa.make_model()
# Add observables
o = Observable('MAPK1p', model.monomers['MAPK1'](T185='p', Y187='p'))
model.add_component(o)
o = Observable('MAPK3p', model.monomers['MAPK3'](T202='p', Y204='p'))
model.add_component(o)
o = Observable('GSK3Ap', model.monomers['GSK3A'](S21='p'))
model.add_component(o)
o = Observable('GSK3Bp', model.monomers['GSK3B'](S9='p'))
model.add_component(o)
o = Observable('RPS6p', model.monomers['RPS6'](S235='p'))
model.add_component(o)
o = Observable('EIF4EBP1p', model.monomers['EIF4EBP1'](S65='p'))
model.add_component(o)
o = Observable('JUNp', model.monomers['JUN'](S73='p'))
model.add_component(o)
o = Observable('FOXO3p', model.monomers['FOXO3'](S315='p'))
model.add_component(o)
o = Observable('AKT1p', model.monomers['AKT1'](S473='p'))
model.add_component(o)
o = Observable('AKT2p', model.monomers['AKT2'](S474='p'))
model.add_component(o)
o = Observable('AKT3p', model.monomers['AKT3'](S='p'))
model.add_component(o)
o = Observable('ELK1', model.monomers['ELK1'](S383='p'))
model.add_component(o)
# Set context
pa.set_context('SKMEL28_SKIN')
pa.save_model(out_file)
ke = KappaExporter(model)
with open('%s.ka' % base_file, 'wb') as fh:
base_file, _ = os.path.splitext(out_file)
fh.write(ke.export().encode('utf-8'))
return model
def test_reduce_activities():
st_out = ac.reduce_activities([st14, st15])
assert (st_out[0].obj_activity == 'kinase')
assert (st_out[1].obj_activity == 'kinase')
def test_reduce_activities():
st_out = ac.reduce_activities([st14, st15])
assert st_out[0].obj_activity == 'kinase'
assert st_out[1].obj_activity == 'kinase'