def nmm_example():
abc = BaseAlphabet.create(b"ACGU", b"X")
basep = BaseLprob.create(abc, (log(0.25), log(0.25), log(0.25), log(0.25)))
codonp = CodonLprob.create(abc)
codonp.set_lprob(Codon.create(b"AUG", abc), log(0.8))
codonp.set_lprob(Codon.create(b"AUU", abc), log(0.1))
B = MuteState.create(b"B", abc)
M1 = FrameState.create(b"M1", basep, CodonMarg.create(codonp), 0.02)
M2 = FrameState.create(b"M2", basep, CodonMarg.create(codonp), 0.01)
E = MuteState.create(b"E", abc)
hmm = HMM.create(abc)
hmm.add_state(B, log(0.5))
hmm.add_state(M1)
hmm.add_state(M2)
hmm.add_state(E)
hmm.set_transition(B, M1, log(0.8))
hmm.set_transition(B, M2, log(0.2))
hmm.set_transition(M1, M2, log(0.1))
hmm.set_transition(M1, E, log(0.4))
hmm.set_transition(M2, E, log(0.3))
dp = hmm.create_dp(E)
return {"hmm": hmm, "dp": dp, "alphabet": abc}
def _create_base_table(codonp: CodonLprob):
base_abc = codonp.alphabet
base_lprob = {base: lprob_zero() for base in base_abc.symbols}
norm = log(3)
for codon in codon_iter(base_abc):
lprob = codonp.get_lprob(codon)
triplet = codon.symbols
base_lprob[triplet[0]] = lprob_add(base_lprob[triplet[0]],
lprob - norm)
base_lprob[triplet[1]] = lprob_add(base_lprob[triplet[1]],
lprob - norm)
base_lprob[triplet[2]] = lprob_add(base_lprob[triplet[2]],
lprob - norm)
assert len(base_lprob) == 4
bases = base_abc.symbols
assert len(bases) == 4
return BaseLprob.create(
base_abc,
(
base_lprob[bases[0]],
base_lprob[bases[1]],
base_lprob[bases[2]],
base_lprob[bases[3]],
),
)
def test_hmm():
abc = BaseAlphabet.create(b"ACGU", b"X")
baset = BaseLprob.create(abc, (log(0.25), log(0.25), log(0.25), log(0.25)))
codonp = CodonLprob.create(abc)
codonp.set_lprob(Codon.create(b"AUG", abc), log(0.8))
codonp.set_lprob(Codon.create(b"AUU", abc), log(0.1))
B = MuteState.create(b"B", abc)
M1 = FrameState.create(b"M1", baset, CodonMarg.create(codonp), 0.02)
M2 = FrameState.create(b"M2", baset, CodonMarg.create(codonp), 0.01)
E = MuteState.create(b"E", abc)
hmm = HMM.create(abc)
hmm.add_state(B, log(0.5))
hmm.add_state(M1)
hmm.add_state(M2)
hmm.add_state(E)
hmm.set_transition(B, M1, log(0.8))
hmm.set_transition(B, M2, log(0.2))
hmm.set_transition(M1, M2, log(0.1))
hmm.set_transition(M1, E, log(0.4))
hmm.set_transition(M2, E, log(0.3))
dp = hmm.create_dp(E)
task = DPTask.create(dp)
task.setup(Sequence.create(b"AUGAUU", abc))
result = dp.viterbi(task)
loglik = hmm.loglikelihood(task.sequence, result.path)
assert_allclose(loglik, -7.069201008427531)
def test_frame_state():
base = BaseAlphabet.create(b"ACGU", b"X")
basep = BaseLprob.create(base,
(log(0.25), log(0.25), log(0.25), log(0.25)))
codonp = CodonLprob.create(base)
codonp.set_lprob(Codon.create(b"AUG", base), log(0.8))
codonp.set_lprob(Codon.create(b"AUU", base), log(0.1))
frame_state = FrameState.create(b"M1", basep, CodonMarg.create(codonp),
0.0)
assert lprob_is_zero(frame_state.lprob(Sequence.create(b"AUA", base)))
assert_allclose(frame_state.lprob(Sequence.create(b"AUG", base)), log(0.8))
assert_allclose(frame_state.lprob(Sequence.create(b"AUU", base)), log(0.1))
assert lprob_is_zero(frame_state.lprob(Sequence.create(b"AU", base)))
assert lprob_is_zero(frame_state.lprob(Sequence.create(b"A", base)))
assert lprob_is_zero(frame_state.lprob(Sequence.create(b"AUUA", base)))
assert lprob_is_zero(frame_state.lprob(Sequence.create(b"AUUAA", base)))
codonp.normalize()
frame_state = FrameState.create(b"M1", basep, CodonMarg.create(codonp),
0.1)
assert_allclose(frame_state.lprob(Sequence.create(b"AUA", base)),
-6.905597115665666)
assert_allclose(frame_state.lprob(Sequence.create(b"AUG", base)),
-0.5347732882047062,
rtol=1e-6)
assert_allclose(frame_state.lprob(Sequence.create(b"AUU", base)),
-2.5902373304999466,
rtol=1e-6)
assert_allclose(frame_state.lprob(Sequence.create(b"AU", base)),
-2.9158434238698336)
assert_allclose(frame_state.lprob(Sequence.create(b"A", base)),
-5.914503505971854)
assert_allclose(frame_state.lprob(Sequence.create(b"AUUA", base)),
-6.881032208841384)
assert_allclose(frame_state.lprob(Sequence.create(b"AUUAA", base)),
-12.08828960987379)
assert lprob_is_zero(frame_state.lprob(Sequence.create(b"AUUAAA", base)))
lprob, codon = frame_state.decode(Sequence.create(b"AUA", base))
assert_allclose(lprob, -7.128586690537968)
assert codon.symbols == b"AUG"
lprob, codon = frame_state.decode(Sequence.create(b"AUAG", base))
assert_allclose(lprob, -4.813151489562624)
assert codon.symbols == b"AUG"
lprob, codon = frame_state.decode(Sequence.create(b"A", base))
assert_allclose(lprob, -6.032286541628237)
assert codon.symbols == b"AUG"
lprob, codon = frame_state.decode(Sequence.create(b"UUU", base))
assert_allclose(lprob, -8.110186062956258)
assert codon.symbols == b"AUU"
def test_codon_state():
base = BaseAlphabet.create(b"ACGU", b"X")
codonp = CodonLprob.create(base)
codonp.set_lprob(Codon.create(b"AUG", base), log(0.8))
codonp.set_lprob(Codon.create(b"AUU", base), log(0.1))
state = CodonState.create(b"M1", codonp)
assert state.name == b"M1"
assert_allclose(state.lprob(Sequence.create(b"AUG", base)), log(0.8))
assert_allclose(state.lprob(Sequence.create(b"AUU", base)), log(0.1))
assert_allclose(state.lprob(Sequence.create(b"ACU", base)), -inf)
def test_codon_marg():
base = BaseAlphabet.create(b"ACGT", b"X")
codonp = CodonLprob.create(base)
codonp.set_lprob(Codon.create(b"AAA", base), log(0.01))
codonp.set_lprob(Codon.create(b"AGA", base), log(0.31))
codonp.set_lprob(Codon.create(b"CAA", base), log(0.40))
codonp.set_lprob(Codon.create(b"CAT", base), log(0.40))
codonm = CodonMarg.create(codonp)
assert_allclose(codonm.lprob(Codon.create(b"CAT", base)), log(0.40))
assert_allclose(codonm.lprob(Codon.create(b"CAX", base)),
log(0.80),
rtol=1e-6)
assert_allclose(codonm.lprob(Codon.create(b"XXX", base)),
log(1.12),
rtol=1e-6)
def test_codon_lprob():
base = BaseAlphabet.create(b"ACGT", b"X")
codonp = CodonLprob.create(base)
with pytest.raises(RuntimeError):
codonp.normalize()
codonp.set_lprob(Codon.create(b"AAA", base), log(0.01))
assert_allclose(codonp.get_lprob(Codon.create(b"AAA", base)), log(0.01))
codonp.normalize()
assert_allclose(codonp.get_lprob(Codon.create(b"AAA", base)), log(1.0))
codonp.set_lprob(Codon.create(b"AAA", base), log(0.01))
assert_allclose(codonp.get_lprob(Codon.create(b"AAA", base)), log(0.01))
assert lprob_is_zero(codonp.get_lprob(Codon.create(b"ACA", base)))
with pytest.raises(RuntimeError):
codonp.get_lprob(Codon.create(b"AXA", base))
def _create_codon_prob(aminot: AminoLprob, gencode: CodonTable) -> CodonLprob:
codonp = CodonLprob.create(gencode.base_alphabet)
codon_lprobs = []
lprob_norm = lprob_zero()
for i in range(len(aminot.alphabet.symbols)):
aa = aminot.alphabet.symbols[i:i + 1]
lprob = aminot.lprob(aa)
codons = gencode.codons(aa)
if len(codons) == 0:
continue
norm = log(len(codons))
for codon in codons:
codon_lprobs.append((codon, lprob - norm))
lprob_norm = lprob_add(lprob_norm, codon_lprobs[-1][1])
for codon, lprob in codon_lprobs:
codonp.set_lprob(codon, lprob - lprob_norm)
return codonp