def test_grow_primers(self):
temp_calculator = TemperatureConfig().create_calculator()
prefix = "TTTTTTTTTTAAAAAC"
overlap = "CGCC"
suffix = "AAAAACTTTTTTTTTT"
temp_thresh_fw = 25.0
temp_thresh_rv = 25.0
overlaps = [SSMPrimerSpec(len(prefix), len(overlap), len(overlap), 0)]
mutations = [AminoMutation(len(prefix), "", "", "", 0)]
sequence = prefix + overlap + suffix
print(sequence)
fw_computed, rv_computed = grow_primers(min(len(prefix),
len(suffix)), 0, sequence,
mutations, overlaps,
temp_thresh_fw, temp_thresh_rv,
temp_calculator)
expected_fw = SSMPrimerSpec(offset=len(prefix),
length=13,
three_end_size=10,
three_end_temp=29.0)
expected_rv = SSMPrimerSpec(offset=5,
length=15,
three_end_size=11,
three_end_temp=28.0)
self.assertEqual(expected_fw, fw_computed[0])
self.assertEqual(expected_rv, rv_computed[0])
def test_grow_reverse_primer(self):
temp_calculator = TemperatureConfig().create_calculator()
max_primer_size = 12
sequence = "AAACCCGGGTTTAAAGGGCCC"
mutation = AminoMutation(10, "", "", "", 0)
overlap = SSMPrimerSpec(10, 3, 0, 0)
primer = grow_reverse_primer(max_primer_size, 0, sequence, mutation,
overlap, 10, temp_calculator)
self.assertEqual(primer.three_end_temp, temp_calculator("CCGGGT"))
self.assertEqual(primer.three_end_size, 6)
self.assertEqual(primer.offset, 4)
def test_grow_reverse_offset(self):
temp_calculator = TemperatureConfig().create_calculator()
prefix = "TTTTTTTTTTAAAAAC"
overlap = "CGCC"
sequence = prefix + overlap
print(sequence)
rv_computed = grow_reverse_primer(
30, 0, sequence, AminoMutation(len(prefix), "", "", "", 0),
SSMPrimerSpec(len(prefix), len(overlap), 0, 0), 25.0,
temp_calculator)
expected_rv = SSMPrimerSpec(offset=5,
length=15,
three_end_size=11,
three_end_temp=28.0)
self.assertEqual(expected_rv, rv_computed)
def step_impl(context, mutation_start):
context.mutation = AminoMutation(mutation_start, "A", "F")
def step_impl(context, mutation_start):
context.five_end_size = context.primer.get_five_end_size_from_mutation(
AminoMutation(mutation_start, "A", "F"))