def test_pattern_and_reverse():
bsmbi = "CGTCTC"
bsmbi_rev = "GAGACG"
sequence = 10 * bsmbi + 25 * bsmbi_rev + 15 * bsmbi + 15 * bsmbi_rev
problem = DnaOptimizationProblem(sequence,
constraints=[AvoidPattern('BsmBI_site')],
objectives=[AvoidChanges()])
problem.resolve_constraints()
problem.optimize()
assert sum(problem.sequence_edits_as_array()) < 70
def test_AvoidRareCodons_as_constraint():
numpy.random.seed(123)
sequence = "ATG" "TTT" "ATA" "CCA" "CTT" "TAG"
problem = DnaOptimizationProblem(
sequence=sequence,
constraints=[EnforceTranslation(),
AvoidRareCodons(0.11, "e_coli")],
)
assert problem.all_constraints_pass()
assert problem.sequence_edits_as_array().sum() == 4
assert translate(problem.sequence) == translate(sequence)
def test_AvoidRareCodons_as_constraint_reversed():
numpy.random.seed(123)
sequence = "ATG" "TTT" "ATA" "CCA" "CTT" "TAG"
rev_sequence = reverse_complement(sequence)
location = (0, len(sequence), -1)
problem = DnaOptimizationProblem(
sequence=rev_sequence,
constraints=[
EnforceTranslation(location=location),
AvoidRareCodons(0.11, "e_coli", location=location),
],
)
assert problem.all_constraints_pass()
assert problem.sequence_edits_as_array().sum() == 4
new_sequence = reverse_complement(problem.sequence)
assert translate(new_sequence) == translate(sequence)
