def test_check_reference_positions2(self):
test_ref_seq = "---------MSPQTETKASVGFKAGVKEYKLTYYTPEYETKDTDILAAFRVTPQPG-----------------" \
"VPPEEAGAAVAAESSTGT---------WTTVWTDGLTSLDRYKG-----RCYHIEPVPG-------------------" \
"EKDQCICYVAYPLDLFEEGSVTNMFTSIVGNVFGFKALRALRLEDLRIPVAYVKTFQGP"
test_positions2 = [50, 63, 75]
adjusted_positions2 = FeaVar.adjust_positions_for_insertions(
test_ref_seq, test_positions2)
test_result = FeaVar.check_reference_positions(test_ref_seq,
adjusted_positions2)
assert test_result is True
def test_check_adjusted_positions(self):
test_ref_seq = "-A--BB---CCC----DDDD"
test_positions1 = [1, 3, 5]
adjusted_positions1 = FeaVar.adjust_positions_for_insertions(
test_ref_seq, test_positions1)
assert adjusted_positions1 == [2, 6, 11]
def test_check_adjusted_positions_right_no_sequence(self):
test_ref_seq = ""
test_positions1 = [1, 3, 5]
adjusted_positions1 = FeaVar.adjust_positions_for_insertions(
test_ref_seq, test_positions1)
assert adjusted_positions1 is None, "No reference sequence"
def test_check_adjusted_positions_right_not_enough_sequence(self):
test_ref_seq = "-A--BB----"
test_positions1 = [1, 3, 5]
adjusted_positions1 = FeaVar.adjust_positions_for_insertions(
test_ref_seq, test_positions1)
assert adjusted_positions1 == [2, 6, 11]
def test_check_adjusted_positions_right_insertions_only(self):
test_ref_seq = "ABBCCCDDDD-----"
test_positions1 = [1, 3, 5]
adjusted_positions1 = FeaVar.adjust_positions_for_insertions(
test_ref_seq, test_positions1)
assert adjusted_positions1 == [1, 3, 5]