def test_base_alphabet():
base = BaseAlphabet.create(b"ACGT", b"X")
assert base.symbols == b"ACGT"
assert str(base) == "{ACGT}"
assert repr(base) == "<BaseAlphabet:{ACGT}>"
with pytest.raises(RuntimeError):
BaseAlphabet.create(b"ACGTK", b"X")
def test_fragment():
alphabet = BaseAlphabet.create(b"ACGT", b"X")
seq = Sequence.create(b"ACAAAGATX", alphabet)
S = MuteState.create(b"S", alphabet)
E = MuteState.create(b"E", alphabet)
M1 = NormalState.create(
b"M1",
alphabet,
[log(0.8), log(0.2), log(0.01),
log(0.01)],
)
M2 = NormalState.create(
b"M2", alphabet,
[log(0.4), log(0.6), log(0.1), log(0.6)])
path = Path.create([
Step.create(S, 0),
Step.create(M1, 1),
Step.create(M2, 1),
Step.create(E, 0)
])
fragment = Fragment(seq, path)
i = iter(fragment)
frag_step = next(i)
assert bytes(frag_step.sequence) == b""
assert frag_step.step.seq_len == 0
assert frag_step.step.state.name == S.name
frag_step = next(i)
assert bytes(frag_step.sequence) == b"A"
assert frag_step.step.seq_len == 1
assert frag_step.step.state.name == M1.name
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_codon_iter():
base = BaseAlphabet.create(b"ACGT", b"X")
codons = list(codon_iter(base))
assert len(codons) == 64
assert codons[0].symbols == b"AAA"
assert codons[1].symbols == b"AAC"
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_base_lprob():
base = BaseAlphabet.create(b"ACGT", b"X")
basep = BaseLprob.create(base, (log(0.1), log(0.2), log(0.3), log(0.4)))
assert_allclose(basep.lprob(b"A"), log(0.1))
assert_allclose(basep.lprob(b"C"), log(0.2))
assert_allclose(basep.lprob(b"G"), log(0.3))
assert_allclose(basep.lprob(b"T"), log(0.4))
with pytest.raises(Exception):
basep = BaseLprob.create(base, (log(0.1), log(0.2), log(0.3)))
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():
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_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))