def test_phos_enz2():
a = Agent('MAP2K1')
b = Agent('PP2A')
st = Dephosphorylation(b, a, 'serine', '222')
s = ea._assemble_modification(st)
print(s)
assert s == 'PP2A dephosphorylates MAP2K1 on S222.'
def test_phos_enz():
a = Agent('MAP2K1')
b = Agent('BRAF')
st = Phosphorylation(b, a, 'serine', '222')
s = ea._assemble_modification(st)
print(s)
assert s == 'BRAF phosphorylates MAP2K1 on S222.'
def test_phos_enz2():
a = Agent('MAP2K1')
b = Agent('PP2A')
st = Dephosphorylation(b, a, 'serine', '222')
s = ea._assemble_modification(st)
print(s)
assert s == 'PP2A dephosphorylates MAP2K1 on S222.'
def test_deubiq_stmt():
st = Deubiquitination(Agent('X'), Agent('Y'))
sb = ea._assemble_modification(st)
print(sb.sentence)
assert sb.sentence == 'X deubiquitinates Y.'
assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'X'
assert _substring_by_coords(sb.sentence, sb.agents[1].coords) == 'Y'
def test_dephos_no_residue():
a = Agent('MAP2K1')
b = Agent('PP2A')
st = Dephosphorylation(b, a, None, '222')
s = ea._assemble_modification(st)
print(s)
assert s == 'PP2A dephosphorylates MAP2K1 at position 222.'
def test_phos_enz():
a = Agent('MAP2K1')
b = Agent('BRAF')
st = Phosphorylation(b, a, 'serine', '222')
s = ea._assemble_modification(st)
print(s)
assert s == 'BRAF phosphorylates MAP2K1 on S222.'
def test_phos_noenz3():
a = Agent('MAP2K1')
st = Phosphorylation(None, a, 'serine', '222')
sb = ea._assemble_modification(st)
print(sb.sentence)
assert sb.sentence == 'MAP2K1 is phosphorylated on S222.'
assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'MAP2K1'
def test_phos_indirect():
a = Agent('MAP2K1')
b = Agent('BRAF')
ev = Evidence(epistemics={'direct': False})
st = Phosphorylation(b, a, 'serine', '222', evidence=[ev])
s = ea._assemble_modification(st)
print(s)
assert s == 'BRAF leads to the phosphorylation of MAP2K1 on S222.'
def test_dephos_no_residue():
a = Agent('MAP2K1')
b = Agent('PP2A')
st = Dephosphorylation(b, a, None, '222')
sb = ea._assemble_modification(st)
print(sb.sentence)
assert sb.sentence == 'PP2A dephosphorylates MAP2K1 at position 222.'
assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'PP2A'
assert _substring_by_coords(sb.sentence, sb.agents[1].coords) == 'MAP2K1'
def test_phos_enz2():
a = Agent('MAP2K1')
b = Agent('PP2A')
st = Dephosphorylation(b, a, 'serine', '222')
sb = ea._assemble_modification(st)
print(sb.sentence)
assert sb.sentence == 'PP2A dephosphorylates MAP2K1 on S222.'
assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'PP2A'
assert _substring_by_coords(sb.sentence, sb.agents[1].coords) == 'MAP2K1'
def test_phos_indirect():
a = Agent('MAP2K1')
b = Agent('BRAF')
ev = Evidence(epistemics={'direct': False})
st = Phosphorylation(b, a, 'serine', '222', evidence=[ev])
sb = ea._assemble_modification(st)
print(sb.sentence)
assert sb.sentence == 'BRAF leads to the phosphorylation of MAP2K1 on S222.'
assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'BRAF'
assert _substring_by_coords(sb.sentence, sb.agents[1].coords) == 'MAP2K1'
def test_phos_noenz3():
a = Agent('MAP2K1')
st = Phosphorylation(None, a, 'serine', '222')
s = ea._assemble_modification(st)
print(s)
assert s == 'MAP2K1 is phosphorylated on S222.'
def test_phos_noenz():
a = Agent('MAP2K1')
st = Phosphorylation(None, a)
s = ea._assemble_modification(st)
print(s)
assert s == 'MAP2K1 is phosphorylated.'
def test_deubiq_noenz():
st = Deubiquitination(None, Agent('Y'))
sb = ea._assemble_modification(st)
print(sb.sentence)
assert sb.sentence == 'Y is deubiquitinated.'
assert _substring_by_coords(sb.sentence, sb.agents[0].coords) == 'Y'
def test_phos_noenz3():
a = Agent('MAP2K1')
st = Phosphorylation(None, a, 'serine', '222')
s = ea._assemble_modification(st)
print(s)
assert s == 'MAP2K1 is phosphorylated on S222.'
def test_deubiq_stmt():
st = Deubiquitination(Agent('X'), Agent('Y'))
s = ea._assemble_modification(st)
print(s)
assert s == 'X deubiquitinates Y.'
def test_deubiq_noenz():
st = Deubiquitination(None, Agent('Y'))
s = ea._assemble_modification(st)
print(s)
assert s == 'Y is deubiquitinated.'
def test_deubiq_stmt():
st = Deubiquitination(Agent('X'), Agent('Y'))
s = ea._assemble_modification(st)
print(s)
assert s == 'X deubiquitinates Y.'
def test_deubiq_noenz():
st = Deubiquitination(None, Agent('Y'))
s = ea._assemble_modification(st)
print(s)
assert s == 'Y is deubiquitinated.'
def test_phos_noenz():
a = Agent('MAP2K1')
st = Phosphorylation(None, a)
s = ea._assemble_modification(st)
print(s)
assert s == 'MAP2K1 is phosphorylated.'
