def test_propose_string(seq):
new_seq = propose(seq)
assert new_seq != seq
assert len(new_seq) == len(seq)
# Check that only one position is different
different_positions = []
for i, (l1, l2) in enumerate(zip(seq, new_seq)):
if l1 != l2:
different_positions.append(i)
assert len(different_positions) == 1
Sequence sampler test.
In this Python script, we start with a sequence,
and try to optimize for a better version of it,
as measured by the sum over reps.
It's a silly task,
but I think it gives us ability to sanity-check that we have
the right thing going.
"""
from jax_unirep import get_reps
from jax_unirep.sampler import is_accepted, propose
starting_sequence = "ASDFGHJKL"
current_sequence = starting_sequence
current_score = get_reps(current_sequence)[0].sum()
sequences = [current_sequence]
scores = [current_score]
for i in range(100):
new_sequence = propose(current_sequence)
new_score = get_reps(new_sequence)[0].sum()
if is_accepted(best=current_score, candidate=new_score, temperature=1):
current_sequence = new_sequence
sequences.append(current_sequence)
print(i, new_sequence, new_score)
def test_propose_wrong_pos_prob_shape():
"""Check that ValueError is raised when pos_prob of wrong shape is added."""
with pytest.raises(ValueError):
new_seq = propose("ADSV", pos_prob=np.array([0.2] * 5))
def test_propose_wrong_pwm_shape():
"""Check that ValueError is raised when pwm of wrong shape is passed in."""
with pytest.raises(ValueError):
new_seq = propose("ASDV", pwm=np.array([0.2] * 5))
def test_propose_empty_string():
"""Check that ValueError is raised with an empty string."""
with pytest.raises(ValueError):
new_seq = propose("")