def test_check_snp_in_primer(self):
"""
Tests snp and no snp in primer sequence
"""
target = get_data_from_csv(data_1)[0]
target.get_target_sequence(target.range)
snp = target.get_snp()
primers_pair = target.design_primers(target.range, target.sequence)
left_primer = Primer(primers_pair["PRIMER_LEFT_0_SEQUENCE"], "left",
primers_pair["PRIMER_LEFT_0"][0], target.range,
target)
right_primer = Primer(primers_pair["PRIMER_RIGHT_0_SEQUENCE"], "right",
primers_pair["PRIMER_RIGHT_0"][0], target.range,
target)
self.assertTrue(left_primer.check_snp_in_primer(snp) == 0)
self.assertTrue(right_primer.check_snp_in_primer(snp) == 0)
def compute_optimal_primers_pairs(self):
"""
Computes a list of primers pairs containing primersPair instance
Use this function to get a list of primers pairs respecting all constraints
with no post-treatment (no BLAST, no sort,...)
:return: a list of primersPair instance.
"""
all_primers_pairs = []
result = self.compute_optimal_raw_primers_pairs()
all_raw_primers_pairs = result[0]
ranges_left = result[1]
SNP = self.get_snp()
for i in range(len(all_raw_primers_pairs)):
left_primer = Primer(
all_raw_primers_pairs[i]["PRIMER_LEFT_0_SEQUENCE"], "left",
all_raw_primers_pairs[i]["PRIMER_LEFT_0"][0], ranges_left[i],
self, all_raw_primers_pairs[i]["PRIMER_LEFT_0_PENALTY"])
right_primer = Primer(
all_raw_primers_pairs[i]["PRIMER_RIGHT_0_SEQUENCE"], "right",
all_raw_primers_pairs[i]["PRIMER_RIGHT_0"][0], ranges_left[i],
self, all_raw_primers_pairs[i]["PRIMER_RIGHT_0_PENALTY"])
if not left_primer.dinucleotides_repeats(
) and not right_primer.dinucleotides_repeats():
if math.fabs(right_primer.TFGP - left_primer.TFGP) <= 90:
if right_primer.check_snp_in_primer(SNP) == 0 and \
left_primer.check_snp_in_primer(SNP) == 0:
primers_pair = PrimersPair(left_primer, right_primer)
if primers_pair not in all_primers_pairs:
all_primers_pairs.append(primers_pair)
self.all_primers_pairs = all_primers_pairs
return all_primers_pairs
