def test_back_adapter_indel_and_mismatch_occurrence():
adapter = BackAdapter(
sequence="GATCGGAAGA",
max_errors=0.1,
min_overlap=3,
)
match = adapter.match_to("CTGGATCGGAGAGCCGTAGATCGGGAGAGGC")
# CTGGATCGGA-GAGCCGTAGATCGGGAGAGGC
# ||||||| || ||||||X|||
# GATCGGAAGA GATCGGAAGA
assert match.errors == 1
assert match.matches == 9
assert match.astart == 0
assert match.astop == 10
assert match.rstart == 3
assert match.rstop == 12
def test_back_adapter_indel_and_exact_occurrence():
adapter = BackAdapter(
sequence="GATCGGAAGA",
max_errors=0.1,
min_overlap=3,
)
match = adapter.match_to("GATCGTGAAGAGATCGGAAGA")
# We want the leftmost match of these two possible ones:
# GATCGTGAAGAGATCGGAAGA
# GATCG-GAAGA
# GATCGGAAGA
assert match.errors == 0
assert match.matches == 10
assert match.astart == 0
assert match.astop == 10
assert match.rstart == 0
assert match.rstop == 10
def test_issue_80():
# This issue turned out to not be an actual issue with the alignment
# algorithm. The following alignment is found because it has more matches
# than the 'obvious' one:
#
# TCGTATGCCGTCTTC
# =========X==XX=
# TCGTATGCCCTC--C
#
# This is correct, albeit a little surprising, since an alignment without
# indels would have only two errors.
adapter = BackAdapter(sequence="TCGTATGCCGTCTTC",
max_errors=0.2,
min_overlap=3,
read_wildcards=False,
adapter_wildcards=False)
result = adapter.match_to("TCGTATGCCCTCC")
assert result.errors == 3, result
assert result.astart == 0, result
assert result.astop == 15, result
def test_back_adapter_partial_occurrence_in_front():
adapter = BackAdapter("CTGAATT", max_errors=0, min_overlap=4)
assert adapter.match_to("AATTGGGGGGG") is None
def test_str():
a = BackAdapter('ACGT', max_errors=0.1)
str(a)
str(a.match_to("TTACGT"))