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test_CodonOptimize.py
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test_CodonOptimize.py
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"""Example of use of the AvoidPAttern specification"""
from dnachisel import (
DnaOptimizationProblem,
random_protein_sequence,
random_dna_sequence,
Location,
CodonOptimize,
reverse_translate,
EnforceTranslation,
biotools,
)
from python_codon_tables import get_codons_table
import numpy
def test_codon_optimize_bestcodon():
numpy.random.seed(123)
protein = random_protein_sequence(3000, seed=123)
sequence = reverse_translate(protein)
problem = DnaOptimizationProblem(
sequence=sequence,
constraints=[EnforceTranslation()],
objectives=[CodonOptimize(species="e_coli")],
logger=None,
)
assert problem.objective_scores_sum() < 0
problem.optimize()
assert problem.objective_scores_sum() == 0
def test_codon_optimize_match_usage_random_sequence():
numpy.random.seed(123)
protein = random_protein_sequence(500, seed=123)
sequence = reverse_translate(protein)
problem = DnaOptimizationProblem(
sequence=sequence,
constraints=[EnforceTranslation()],
objectives=[
CodonOptimize(species="e_coli", method="match_codon_usage")
],
logger=None,
)
assert -600 < problem.objective_scores_sum() < -550
problem.optimize()
print (problem.objective_scores_sum())
assert -17 < problem.objective_scores_sum()
def test_codon_optimize_match_usage_gfp_sequence():
sequence = (
"ATGGTGAGCAAGGGCGAGGAGCTGTTCACCGGGGTGGTGCCCATCCTG"
"GTCGAGCTGGACGGCGACGTAAACGGCCACAAGTTCAGCGTGCGCGGC"
"GAGGGCGAGGGCGATGCCACCAACGGCAAGCTGACCCTGAAGTTCATC"
)
spec = CodonOptimize(species="s_cerevisiae", method="match_codon_usage")
problem = DnaOptimizationProblem(
sequence=sequence,
constraints=[EnforceTranslation()],
objectives=[spec],
logger=None,
)
assert problem.objective_scores_sum() < -61
problem.optimize()
assert problem.objective_scores_sum() > -16
# Just for coverage, we run the compare_frequency function in text mode
spec = problem.objectives[0]
codons = spec.get_codons(problem)
print(spec.compare_frequencies(codons, text_mode=True))
def test_codon_optimize_match_usage_short_sequence():
numpy.random.seed(123)
protein = "DDDKKKKKK"
sequence = reverse_translate(protein)
harmonization = CodonOptimize(
species="b_subtilis", method="match_codon_usage"
)
problem = DnaOptimizationProblem(
sequence=sequence,
constraints=[EnforceTranslation()],
objectives=[harmonization],
logger=None,
)
assert problem.objective_scores_sum() < -5.5
problem.optimize()
assert -0.6 < problem.objective_scores_sum()
print(problem.objective_scores_sum())
assert problem.sequence == "GATGATGACAAGAAAAAGAAAAAAAAA"
def test_codon_optimize_harmonize_rca_short_sequence():
protein = random_protein_sequence(500, seed=123)
sequence = reverse_translate(protein)
harmonization = CodonOptimize(
species="h_sapiens", original_species="e_coli", method="harmonize_rca"
)
problem = DnaOptimizationProblem(
sequence=sequence,
constraints=[EnforceTranslation()],
objectives=[harmonization],
logger=None,
)
assert problem.objective_scores_sum() < -123
problem.optimize()
assert -74 < problem.objective_scores_sum()
def test_codon_optimize_as_hard_constraint():
numpy.random.seed(123)
problem = DnaOptimizationProblem(
sequence=random_dna_sequence(2000, seed=123),
constraints=[
EnforceTranslation(location=Location(1000, 1300)),
CodonOptimize(location=Location(1000, 1300), species="e_coli"),
],
logger=None,
)
assert not problem.all_constraints_pass()
problem.resolve_constraints()
assert problem.all_constraints_pass()
def test_codon_optimize_with_custom_table():
table = get_codons_table("b_subtilis")
problem = DnaOptimizationProblem(
sequence=random_dna_sequence(1200, seed=123),
constraints=[EnforceTranslation()],
objectives=[CodonOptimize(codon_usage_table=table)],
logger=None,
)
assert problem.objective_scores_sum() < -10
problem.optimize()
assert problem.objective_scores_sum() == 0