def solver_with_input(inputs, use_fast_approximation_algorithm):
goi, plasmid, mutations = inputs
config = create_test_config(goi, plasmid, mutations,
use_fast_approximation_algorithm)
start = time()
solution = ssm_solve(config, NullPrimerGenerator(), AllPrimerGenerator())
end = time()
return stats_dataframe_for_solution(solution, end - start)
class SsmSolveTestSpecificConfigsRandom16(SsmSolveTestConfigRange):
secondary_generator = AllPrimerGenerator()
initialized = False
percentage = 0.59
num_of_tests = 0
separate_temp_calc = True
exclude_fl_prim = True
primary_generator = Primer3(primer3_path=PRIMER3_PATH)
use_fast_approximation = False
hairpins = False
class SsmSolveTestSpecificConfigsRandom14(SsmSolveTestConfigRange):
secondary_generator = AllPrimerGenerator()
initialized = False
percentage = 0.9
num_of_tests = 10
separate_temp_calc = True
exclude_fl_prim = True
primary_generator = NullPrimerGenerator()
use_fast_approximation = True
hairpins = False
from mutation_maker.ssm import ssm_solve
from mutation_maker.qclm import qclm_solve, QCLMInput, QCLMOutput
from mutation_maker.primer3_interoperability import Primer3, AllPrimerGenerator, NullPrimerGenerator
from mutation_maker.ssm_types import SSMInput, SSMOutput
from mutation_maker.pas import pas_solve
from mutation_maker.pas_types import PASInput
print("Mutation Maker version: 1.0.0")
PRIMER3_PATH = os.environ.get('PRIMER3HOME')
CELERY_BROKER_URL = os.environ.get('CELERY_BROKER_URL', 'redis://*****:*****@celery.task(name='tasks.ssm')
def ssm(ssm_input):
data = parse_body(ssm_input)
input = SSMInput(data)
if input.config.use_primer3:
main_generator = primer3
else:
main_generator = NullPrimerGenerator()
return ssm_solve(input, main_generator, secondary_generator)
class SsmSolveTestConfigRange(unittest.TestCase):
"""
Run tests with null generator as primary generator on random examples
"""
percentage = 0.9
primary_generator = Primer3(primer3_path=PRIMER3_PATH)
secondary_generator = AllPrimerGenerator()
use_fast_approximation = True
exclude_fl_prim = False
initialized = False
hairpins = False
separate_temp_calc = True
num_of_tests = 1
@classmethod
def initialize(cls):
max_muts = 24
if not cls.initialized:
# b_tmp = [True, False]
# primary_generators = [Primer3(primer3_path=PRIMER3_PATH), NullPrimerGenerator()]
# # all configurations
# for use_fast_approximation in b_tmp:
# for exclude_fl_prim in b_tmp:
# for p_generator in primary_generators:
random.seed(123)
tst_start = 0
tst_end = cls.num_of_tests
cls.results = []
for ind in range(tst_start, tst_end):
print(f"\nRandom result NO. {ind+1} generated.\n")
cls.results.append(
ssm_solve(
generate_random_SSM_input(
mut_cnt=random.randint(12, max_muts),
use_fast_approximation=cls.use_fast_approximation,
exclude_fl_prim=cls.exclude_fl_prim,
hairpins=cls.hairpins,
separate=cls.separate_temp_calc),
cls.primary_generator, cls.secondary_generator))
cls.initialized = True
def test_primer_size(self):
self.__class__.initialize()
cnt = 0
for result in self.__class__.results:
# test primer size
if test_primer_size_in_range(result):
cnt += 1
self.assertGreaterEqual(
cnt,
len(self.__class__.results) * self.__class__.percentage,
"Too many primers out of range")
if len(self.__class__.results) > 0:
print("%.2f of primers have size in range." %
(cnt / len(self.__class__.results) * 100))
def test_3_end_size(self):
self.__class__.initialize()
cnt = 0
for result in self.__class__.results:
# test primer size
if test_3end_size_in_range(result):
cnt += 1
self.assertGreaterEqual(
cnt,
len(self.__class__.results) * self.__class__.percentage,
"Too many primers 3 end size out of range")
if len(self.__class__.results) > 0:
print("%.2f of primers have 3 end size in range." %
(cnt / len(self.__class__.results) * 100))
def test_5_end_size(self):
self.__class__.initialize()
cnt = 0
for result in self.__class__.results:
# test primer size
if test_5end_size_in_range(result):
cnt += 1
self.assertGreaterEqual(
cnt,
len(self.__class__.results) * self.__class__.percentage,
"Too many primers 5 end size out of range")
if len(self.__class__.results) > 0:
print("%.2f of primers have 5 end size in range." %
(cnt / len(self.__class__.results) * 100))
def test_overlap_size(self):
self.__class__.initialize()
cnt = 0
for result in self.__class__.results:
# test primer size
if test_overlap_size_in_range(result):
cnt += 1
self.assertGreaterEqual(
cnt,
len(self.__class__.results) * self.__class__.percentage,
"Too many primers overlap size is out of range!")
if len(self.__class__.results) > 0:
print("%.2f of primers have overlap size in range." %
(cnt / len(self.__class__.results) * 100))
def test_overlap_temp(self):
self.__class__.initialize()
cnt = 0
for result in self.__class__.results:
# test primer size
if test_overlap_temperature_in_range(result):
cnt += 1
self.assertGreaterEqual(
cnt, 0, "Too many primers overlap temperature is out of range!")
if len(self.__class__.results) > 0:
print("%.2f of primers have overlap temp. in range." %
(cnt / len(self.__class__.results) * 100))
def test_3_end_temp(self):
self.__class__.initialize()
cnt = 0
for result in self.__class__.results:
# test primer size
if test_3end_temperature_in_range(result):
cnt += 1
self.assertGreaterEqual(
cnt,
len(self.__class__.results) * self.__class__.percentage,
"Too many primers 3 end temperatures out of range")
if len(self.__class__.results) > 0:
print("%.2f of primers have 3'end temp. in range." %
(cnt / len(self.__class__.results) * 100))
def test_overlap_complementary(self):
self.__class__.initialize()
cnt = 0
for result in self.__class__.results:
# test primer size
if test_overlap_complementary(result):
cnt += 1
self.assertGreaterEqual(
cnt,
len(self.__class__.results) * self.__class__.percentage,
"Too many primers overlap size is incorrectly computed")
if len(self.__class__.results) > 0:
print("%.2f of primers are correctly complements to each other." %
(cnt / len(self.__class__.results) * 100))
def test_mutation_position(self):
self.__class__.initialize()
cnt = 0
for result in self.__class__.results:
# test primer size
if test_mutation_position(result):
cnt += 1
self.assertGreaterEqual(
cnt,
len(self.__class__.results) * self.__class__.percentage,
"Too many primers mutation is not on expected location!")
if len(self.__class__.results) > 0:
print("%.2f of primers mutation at right spot." %
(cnt / len(self.__class__.results) * 100))
class SsmSolveTestOnPresetPrimer3(unittest.TestCase):
initialized = False
primary_generator = Primer3(primer3_path=PRIMER3_PATH)
secondary_generator = AllPrimerGenerator()
use_fast_approximation = True
exclude_fl_prim = True
@classmethod
def initialize(cls):
if not cls.initialized:
tst_start = 0
tst_end = 10
cls.results = []
for ind in range(tst_start, tst_end):
print(f"\nPreset result NO. {ind+1} generated.\n")
cls.results.append(
ssm_solve(
generate_SSM_input(
ind,
primer_growth=cls.use_fast_approximation,
separateTM=cls.exclude_fl_prim),
cls.primary_generator, cls.secondary_generator))
cls.initialized = True
def test_primer_size(self):
self.__class__.initialize()
for result in self.__class__.results:
# test primer size
self.assertTrue(test_primer_size_in_range(result),
msg="Primer size is out of range!")
def test_3_end_size(self):
self.__class__.initialize()
for result in self.__class__.results:
self.assertTrue(test_3end_size_in_range(result),
msg="Primers 3'end size is out of range!")
def test_overlap_size(self):
self.__class__.initialize()
for result in self.__class__.results:
# test overlap size
self.assertTrue(test_overlap_size_in_range(result),
msg="Overlap size is out of range!")
def test_overlap_temp(self):
self.__class__.initialize()
for result in self.__class__.results:
# test overlap temperature in range
self.assertTrue(test_overlap_temperature_in_range(result),
msg="Overlap temperature is out of range!")
def test_3_end_temp(self):
self.__class__.initialize()
for result in self.__class__.results:
# test 3'end temperature of primers
self.assertTrue(test_3end_temperature_in_range(result),
msg="Primer 3'end temperature is out of range!")
def test_overlap_complementary(self):
self.__class__.initialize()
for result in self.__class__.results:
# test overlap complementary
self.assertTrue(test_overlap_complementary(result),
msg="Overlap size is incorrectly computed!")
def test_mutation_position(self):
self.__class__.initialize()
for result in self.__class__.results:
# test mutation position
self.assertTrue(test_mutation_position(result),
msg="Mutation is not on expected location!")
def test_min_5_end_size(self):
self.__class__.initialize()
for result in self.__class__.results:
# test mutation position
self.assertTrue(test_5end_size_in_range(result),
msg="Primers do not have sufficient 5 end size!")