def test_ssm_sequence_wrong_multiple_goi(self):
"""
Scenario desc: Gene of interest is found multiple times in the plasmid. We expect error.
"""
sequences = SSMSequences(
forward_primer=fw_primer_short,
reverse_primer=rv_primer_short,
gene_of_interest=goi_short,
plasmid=Plasmid(plasmid_sequence=plasmid_seq_short + goi_short))
with self.assertRaises(ValueError) as context:
sequences.get_full_sequence_with_offset()
self.assertTrue(
'Gene of interest position is ambiguous' in str(context.exception))
def test_ssm_sequence_complex_valid(self):
"""
Scenario desc: Checking creation of full sequence and finding the offset for
long sequence (length=1747)
"""
sequences = SSMSequences(forward_primer=fw_primer,
reverse_primer=rv_primer,
gene_of_interest=gene_of_interest,
plasmid=Plasmid(plasmid_sequence=plasmid_seq))
result_full_seq, offsets = sequences.get_full_sequence_with_offset()
self.assertEqual(result_full_seq, full_seq)
self.assertEqual(offsets, (316, 1747))
def test_ssm_sequence_wrong_rv_primer(self):
"""
Scenario desc: Complement to reverse primer is not found in sequence. We expect error.
"""
sequences = SSMSequences(
forward_primer=fw_primer_short,
reverse_primer="CCC",
gene_of_interest=goi_short,
plasmid=Plasmid(plasmid_sequence=plasmid_seq_short))
with self.assertRaises(ValueError) as context:
sequences.get_full_sequence_with_offset()
self.assertTrue('Reverse primer was not found in plasmid' in str(
context.exception))
def test_ssm_sequence_missing_goi(self):
"""
Scenario desc: Gene of interest is not found in sequence. We expect error.
"""
sequences = SSMSequences(
forward_primer=fw_primer_short,
reverse_primer=rv_primer_short,
gene_of_interest="GGG",
plasmid=Plasmid(plasmid_sequence=plasmid_seq_short))
with self.assertRaises(ValueError) as context:
sequences.get_full_sequence_with_offset()
self.assertTrue('Gene of interest was not found in plasmid' in str(
context.exception))
def test_ssm_sequence_valid_cyclic_seq(self):
"""
Scenario desc: check offset computation and g.o.i. look-up in cyclic sequence.
Sequence has same start/end so here we look more at creating the full sequence.
"""
sequences = SSMSequences(forward_primer="AAT",
reverse_primer="GGC",
gene_of_interest="CCC",
plasmid=Plasmid(plasmid_sequence="AAA" +
plasmid_seq_short + "AAA"))
result_full_seq, offsets = sequences.get_full_sequence_with_offset()
self.assertEqual(result_full_seq, "AATGTCAAACCCTTTGCC")
self.assertEqual(offsets, (9, 12))
def test_ssm_sequence_simple_valid(self):
"""
Scenario desc: check offset computation and g.o.i. look-up in simple sequence.
:return:
"""
sequences = SSMSequences(
forward_primer=fw_primer_short,
reverse_primer=rv_primer_short,
gene_of_interest="AAA",
plasmid=Plasmid(plasmid_sequence=plasmid_seq_short))
result_full_seq, offsets = sequences.get_full_sequence_with_offset()
self.assertEqual(result_full_seq, "AATGTCAAACCCTTTGCC")
self.assertEqual(offsets, (6, 9))
def test_ssm_sequence_simple_valid_rev(self):
"""
Scenario desc: check offset computation and g.o.i. look-up in simple sequence.
This time the forward primer is after reverse primer in sequence.
:return:
"""
sequences = SSMSequences(
forward_primer="GCC",
reverse_primer="TTT",
gene_of_interest="GTC",
plasmid=Plasmid(plasmid_sequence="AATGTCAAACCCTTTGCC"))
result_full_seq, offsets = sequences.get_full_sequence_with_offset()
self.assertEqual(result_full_seq, "GCCAATGTCAAA")
self.assertEqual(offsets, (6, 9))
def __init__(self, ssm_sequences: SSMSequences, ssm_config: SSMConfig,
main_primer_generator: PrimerGenerator,
secondary_primer_generator: PrimerGenerator) -> None:
self.main_primer_generator = main_primer_generator
self.secondary_primer_generator = secondary_primer_generator
self.config = ssm_config
self.temp_calculator = ssm_config.temperature_config.create_calculator(
)
if self.temp_calculator.precision > 1:
raise ValueError(
"""Temperature calculation for SSM with precision of more than one decimal place \
is not needed and have severe negative impact on performance""")
self.gc_settings = MinOptMax(self.config.min_gc_content,
self.config.opt_gc_content,
self.config.max_gc_content)
self.forward_primer = ssm_sequences.forward_primer
self.reverse_primer = ssm_sequences.reverse_primer
self.forward_primer_temp = self.temp_calculator(self.forward_primer)
self.reverse_primer_temp = self.temp_calculator(self.reverse_primer)
self.three_end_pivot_temps = [
self.forward_primer_temp, self.reverse_primer_temp
]
self.sequence, self.goi_range = ssm_sequences.get_full_sequence_with_offset(
)
self.flanks = SSMFlankingSequences(ssm_sequences.forward_primer,
ssm_sequences.reverse_primer)
def sample_ssm_sequence():
return SSMSequences(
forward_primer="PLACE_YOUR_OWN_SEQUENCE_FOR_TESTING",
reverse_primer="PLACE_YOUR_OWN_SEQUENCE_FOR_TESTING",
gene_of_interest="PLACE_YOUR_OWN_SEQUENCE_FOR_TESTING",
plasmid=Plasmid(
plasmid_sequence="PLACE_YOUR_OWN_SEQUENCE_FOR_TESTING"))
def test_ssm_sequence_goi_outside_primers(self):
"""
Scenario desc: Gene of interest is not found between forward
and revers primer. We expect error.
Plasmid sequence: AAT GTC AAA CCC TTT GCC
Forward primer: AAT
Reverse primer: AAA (reverse is TTT)
Gene of interest: GCC (which is after TTT)
Sequence specified by primers should be: AAT GTC AAA CCC TTT
"""
sequences = SSMSequences(
forward_primer=fw_primer_short,
reverse_primer="AAA",
gene_of_interest="GCC",
plasmid=Plasmid(plasmid_sequence=plasmid_seq_short))
with self.assertRaises(ValueError) as context:
sequences.get_full_sequence_with_offset()
self.assertTrue('Gene of interest was not found in plasmid' in str(
context.exception))
def create_test_config(goi, plasmid, mutations,
use_fast_approximation_algorithm):
ssm_data = SSMInput(
sequences=SSMSequences(
forward_primer="PLACE_YOUR_OWN_SEQUENCE_FOR_TESTING",
reverse_primer="PLACE_YOUR_OWN_SEQUENCE_FOR_TESTING",
gene_of_interest=goi,
plasmid=Plasmid(plasmid_sequence=plasmid, )),
config=SSMConfig(
calculation_method="MaxMutationsCovered",
max_three_end_ranges=1,
temperature_config=TemperatureConfig(precision=0),
use_fast_approximation_algorithm=use_fast_approximation_algorithm),
mutations=mutations)
return ssm_data