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 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 __init__(
self,
base_abc: Union[DNAAlphabet, RNAAlphabet],
amino_abc: AminoAlphabet,
gencode: Optional[GeneticCode] = None,
):
self._base_alphabet = base_abc
self._amino_alphabet = amino_abc
if gencode is None:
gencode = GeneticCode("Standard")
table = translation_table(gencode)
def replace(seq: bytes):
if isinstance(base_abc, RNAAlphabet):
seq = seq.replace(b"T", b"U")
return seq
self._codons: Dict[bytes, List[Codon]] = {}
self._start_codons = []
for t, a in table.forward_table.items():
triplet = replace(t.encode())
aa = a.encode()
if aa not in self._codons:
self._codons[aa] = []
codon = Codon.create(triplet, base_abc)
if t in table.start_codons:
self._start_codons.append(codon)
self._codons[aa].append(codon)
self._amino_acid: Dict[Codon, bytes] = {}
for aa, codons in self._codons.items():
for codon in codons:
self._amino_acid[codon] = aa
self._stop_codons = []
for t in table.stop_codons:
triplet = replace(t.encode())
self._stop_codons.append(Codon.create(triplet, base_abc))
assert len(self._amino_acid) <= 64
assert len(self._amino_acid) + len(self._stop_codons) == 64
def null_amino_stream(self):
base_abc = self._codon_table.base_alphabet
cstream = self.null_codon_stream
aminos = []
for i in range(0, len(cstream), 3):
codon = Codon.create(cstream[i : i + 3].encode(), base_abc)
amino = self._codon_table.amino_acid(codon)
aminos.append(amino.decode())
return "".join(aminos)
def test_codon():
base = BaseAlphabet.create(b"ACGT", b"X")
codon = Codon.create(b"AAA", base)
assert codon.symbols == b"AAA"
codon.symbols = b"GTX"
assert codon.symbols == b"GTX"
with pytest.raises(ValueError):
codon.symbols = b"GTGG"
with pytest.raises(ValueError):
codon.symbols = b"GT"
with pytest.raises(ValueError):
codon.symbols = b"ADA"
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))