def test_match_probability():
a = InsertAligner('TTAGACATAT', 'CAGTGGAGTA')
k = 3
n = 5
i3 = (120 / (6 * 2)) * (0.25 ** 3) * (0.75 ** 2)
i4 = (120 / 24) * (0.25 ** 4) * 0.75
i5 = 0.25 ** 5
assert approx_equal(a.match_probability(k, n), i3 + i4 + i5, 0.0001)
def test_short_adapter_overlap():
a1_seq = 'TTAGACATAT'
a2_seq = 'CAGTGGAGTA'
seq1 = 'GACAGGCCGTTTGAATGTTGACGGGATGTT'
seq2 = 'CATCCCGTCAACATTCAAACGGCCTGTCCA'
aligner = InsertAligner(a1_seq, a2_seq)
insert_match, match1, match2 = aligner.match_insert(seq1, seq2)
assert match1.rstart == 28
assert match1.length == 2
assert match2.rstart == 28
assert match2.length == 2
def test_insert_align():
a1_seq = 'TTAGACATATGG'
a2_seq = 'CAGTGGAGTATA'
aligner = InsertAligner(a1_seq, a2_seq)
r1 = 'AGTCGAGCCCATTGCAGACT' + a1_seq[0:10]
r2 = 'AGTCTGCAATGGGCTCGACT' + a2_seq[0:10]
insert_match, match1, match2 = aligner.match_insert(r1, r2)
assert match1.rstart == 20
assert match1.length == 10
assert match2.rstart == 20
assert match2.length == 10
def __init__(
self, adapter1, adapter2, action='trim', mismatch_action=None,
symmetric=True, min_insert_overlap=1, **aligner_args):
ErrorCorrectorMixin.__init__(self, mismatch_action)
self.adapter1 = adapter1
self.adapter2 = adapter2
self.aligner = InsertAligner(
adapter1.sequence, adapter2.sequence,
min_insert_overlap=min_insert_overlap, **aligner_args)
self.min_insert_len = min_insert_overlap
self.action = action
self.symmetric = symmetric
self.with_adapters = [0, 0]
