def test_optimization_2():
sequence_path = os.path.join("tests", "data",
"test_optimization_sequence_2.fa")
sequence = str(load_record(sequence_path).seq)[:5500]
deluxe_dna = CommercialDnaOffer(
name="DeluxeDNA.com",
sequence_constraints=[SequenceLengthConstraint(max_length=4000)],
pricing=PerBasepairPricing(0.20),
lead_time=10,
)
cheap_dna = CommercialDnaOffer(
name="CheapDNA.com",
sequence_constraints=[
NoPatternConstraint(enzyme="BsaI"),
EnforceGCContent(0.3, 0.7, window=60),
],
pricing=PerBasepairPricing(0.10),
lead_time=15,
)
# BLOCKS TO CHUNKS ASSEMBLY
gibson_blocks_assembly_station = DnaAssemblyStation(
name="Gibson Blocks Assembly",
assembly_method=GibsonAssemblyMethod(
overhang_selector=FixedSizeSegmentSelector(10),
min_segment_length=1000,
max_segment_length=6000,
duration=8,
cost=16,
),
supplier=[deluxe_dna, cheap_dna],
coarse_grain=30,
fine_grain=False,
memoize=True,
# a_star_factor="auto",
)
quote_before = gibson_blocks_assembly_station.get_quote(sequence)
assert quote_before.price > 850
objective = OptimizeManufacturability(gibson_blocks_assembly_station)
problem = DnaOptimizationProblem(
sequence=sequence,
constraints=[EnforceTranslation(location=(0, 4998))],
objectives=[objective],
)
problem.randomization_threshold = 0 # Forces "random search" mode
problem.max_random_iters = 5
problem.optimize()
print("OPTIMIZATION DONE, GENERATING REPORT")
quote_after = gibson_blocks_assembly_station.get_quote(problem.sequence)
assert quote_after.price < 580
def test_optimization_1():
company_ingen = CommercialDnaOffer(
name="Company InGen",
pricing=PerBasepairPricing(0.08),
sequence_constraints=[NoPatternConstraint(enzyme="AarI")],
)
company_delux = CommercialDnaOffer(
name="Company Delux",
pricing=PerBasepairPricing(0.66),
sequence_constraints=[],
)
assembly_station = DnaAssemblyStation(
name="Gibson Assembly Station",
assembly_method=GibsonAssemblyMethod(
overhang_selector=FixedSizeSegmentSelector(20),
min_segment_length=200,
max_segment_length=1200,
),
supplier=[company_ingen, company_delux],
coarse_grain=20,
# a_star_factor="auto",
)
sequence_path = os.path.join("tests", "data",
"test_optimization_sequence_1.fa")
sequence = load_record(sequence_path)
objective = OptimizeManufacturability(assembly_station)
problem = DnaOptimizationProblem(sequence=sequence, objectives=[objective])
quote = objective.get_quote(problem)
score = problem.objective_scores_sum()
assert -367 < score < -366
problem.randomization_threshold = 0
problem.max_random_iters = 5
problem.optimize()
score = problem.objective_scores_sum()
assert -244 < score < -243
