def test_translocation():
st1 = Translocation(Agent('FOXO3A'))
st2 = Translocation(Agent('FOXO3A'), 'cytoplasm')
st3 = Translocation(Agent('FOXO3A'), None, 'nucleus')
st4 = Translocation(Agent('FOXO3A'), 'cytoplasm', 'nucleus')
e = ea.EnglishAssembler()
e.add_statements([st1])
s = e.make_model()
assert s == 'FOXO3A translocates.'
assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'FOXO3A'
e = ea.EnglishAssembler()
e.add_statements([st2])
s = e.make_model()
assert s == 'FOXO3A translocates from the cytoplasm.'
assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'FOXO3A'
e = ea.EnglishAssembler()
e.add_statements([st3])
s = e.make_model()
assert s == 'FOXO3A translocates to the nucleus.'
assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'FOXO3A'
e = ea.EnglishAssembler()
e.add_statements([st4])
s = e.make_model()
assert s == 'FOXO3A translocates from the cytoplasm to the nucleus.'
assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'FOXO3A'
def test_agent_activity_stmt():
braf = Agent('BRAF', activity=ActivityCondition('activity', True))
mek = Agent('MAP2K1')
st = Activation(braf, mek)
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert s == 'Active BRAF activates MAP2K1.'
def test_agent_activity_stmt():
braf = Agent('BRAF', activity=ActivityCondition('activity', True))
mek = Agent('MAP2K1')
st = Activation(braf, mek)
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
assert s == 'Active BRAF activates MAP2K1.'
assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'BRAF'
assert _substring_by_coords(s, e.stmt_agents[0][1].coords) == 'MAP2K1'
def test_translocation():
st1 = Translocation(Agent('FOXO3A'))
st2 = Translocation(Agent('FOXO3A'), 'cytoplasm')
st3 = Translocation(Agent('FOXO3A'), None, 'nucleus')
st4 = Translocation(Agent('FOXO3A'), 'cytoplasm', 'nucleus')
e = ea.EnglishAssembler()
e.add_statements([st1])
s = e.make_model()
assert s == 'FOXO3A translocates.'
e = ea.EnglishAssembler()
e.add_statements([st2])
s = e.make_model()
assert s == 'FOXO3A translocates from the cytoplasm.'
e = ea.EnglishAssembler()
e.add_statements([st3])
s = e.make_model()
assert s == 'FOXO3A translocates to the nucleus.'
e = ea.EnglishAssembler()
e.add_statements([st4])
s = e.make_model()
assert s == 'FOXO3A translocates from the cytoplasm to the nucleus.'
def test_assemble_more():
a = Agent('MAP2K1')
b = Agent('PP2A')
st1 = Dephosphorylation(b, a, 'serine', 222)
b = Agent('BRAF')
c = Agent('RAF1')
st2 = Complex([a, b, c])
e = ea.EnglishAssembler()
e.add_statements([st1, st2])
s = e.make_model()
print(s)
assert s == \
'PP2A dephosphorylates MAP2K1 on S222. MAP2K1 binds BRAF and RAF1.'
def test_assemble_more():
a = Agent('MAP2K1')
b = Agent('PP2A')
st1 = Dephosphorylation(b, a, 'serine', 222)
b = Agent('BRAF')
c = Agent('RAF1')
st2 = Complex([a, b, c])
e = ea.EnglishAssembler()
e.add_statements([st1, st2])
s = e.make_model()
print(s)
assert s == \
'PP2A dephosphorylates MAP2K1 on S222. MAP2K1 binds BRAF and RAF1.'
assert _substring_by_coords(s, e.stmt_agents[0][0].coords) == 'PP2A'
assert _substring_by_coords(s, e.stmt_agents[0][1].coords) == 'MAP2K1'
assert _substring_by_coords(s, e.stmt_agents[1][0].coords) == 'MAP2K1'
assert _substring_by_coords(s, e.stmt_agents[1][1].coords) == 'BRAF'
assert _substring_by_coords(s, e.stmt_agents[1][2].coords) == 'RAF1'
def _stmt_to_text(st):
e = ea.EnglishAssembler()
e.add_statements([st])
s = e.make_model()
print(s)
return s