def test_indexed_too_high_k():
with pytest.raises(ValueError) as e:
IndexedPrefixAdapters([
PrefixAdapter("ACGTACGT", max_errors=3, indels=False),
PrefixAdapter("AAGGTTCC", max_errors=2, indels=False),
])
assert "Error rate too high" in e.value.args[0]
def test_multi_prefix_adapter_with_indels():
adapters = [
PrefixAdapter("GTAC", max_errors=1, indels=True),
PrefixAdapter("TGCT", max_errors=1, indels=True),
]
ma = IndexedPrefixAdapters(adapters)
match = ma.match_to("GATACGGG")
assert match.adapter is adapters[0]
match = ma.match_to("TAGCTAA")
assert match.adapter is adapters[1]
def test_indexed_prefix_adapters():
adapters = [
PrefixAdapter("GAAC", indels=False),
PrefixAdapter("TGCT", indels=False),
]
ma = IndexedPrefixAdapters(adapters)
match = ma.match_to("GAACTT")
assert match.adapter is adapters[0]
match = ma.match_to("TGCTAA")
assert match.adapter is adapters[1]
def test_multi_prefix_adapter():
adapters = [
PrefixAdapter("GAAC", indels=False),
PrefixAdapter("TGCT", indels=False),
]
ma = MultiPrefixAdapter(adapters)
match = ma.match_to("GAACTT")
assert match.adapter is adapters[0]
match = ma.match_to("TGCTAA")
assert match.adapter is adapters[1]
def test_prefix_with_indels_two_mismatches():
a = PrefixAdapter(
sequence="GCACATTT",
max_errors=0.3,
min_overlap=1,
read_wildcards=False,
adapter_wildcards=False,
indels=True,
)
result = a.match_to("GCACATCGGAA")
assert result.errors == 2
assert result.matches == 6
assert result.astart == 0
assert result.astop == 8
assert result.rstart == 0
assert result.rstop == 8
def test_reverse_complementer():
adapters = [
PrefixAdapter("TTATTTGTCT"),
PrefixAdapter("TCCGCACTGG"),
]
adapter_cutter = AdapterCutter(adapters, index=False)
reverse_complementer = ReverseComplementer(adapter_cutter)
read = Sequence("r", "ttatttgtctCCAGCTTAGACATATCGCCT")
info = ModificationInfo(read)
trimmed = reverse_complementer(read, info)
assert trimmed.sequence == "CCAGCTTAGACATATCGCCT"
assert not info.is_rc
read = Sequence("r", "CAACAGGCCACATTAGACATATCGGATGGTagacaaataa")
info = ModificationInfo(read)
trimmed = reverse_complementer(read, info)
assert trimmed.sequence == "ACCATCCGATATGTCTAATGTGGCCTGTTG"
assert info.is_rc
def test_indexed_prefix_adapters_with_n_wildcard():
sequence = "GGTCCAGA"
ma = IndexedPrefixAdapters([PrefixAdapter(sequence, max_errors=1, indels=False)])
for i in range(len(sequence)):
t = sequence[:i] + "N" + sequence[i+1:] + "TGCT"
result = ma.match_to(t)
assert isinstance(result, RemoveBeforeMatch)
assert (result.rstart, result.rstop) == (0, 8)
assert result.errors == 1
assert result.matches == 7
def test_adapter_cutter_indexing():
adapters = [
PrefixAdapter(sequence, max_errors=1, indels=False) for sequence in
["ACGAT", "GGAC", "TTTACTTA", "TAACCGGT", "GTTTACGTA", "CGATA"]
]
ac = AdapterCutter(adapters)
assert len(ac.adapters) == 1
assert isinstance(ac.adapters[0], IndexedPrefixAdapters)
ac = AdapterCutter(adapters, index=False)
assert len(ac.adapters) == len(adapters)
def test_linked_adapter():
front_adapter = PrefixAdapter('AAAA', min_overlap=4)
back_adapter = BackAdapter('TTTT', min_overlap=3)
linked_adapter = LinkedAdapter(
front_adapter, back_adapter, front_required=True, back_required=False, name='name')
assert linked_adapter.front_adapter.min_overlap == 4
assert linked_adapter.back_adapter.min_overlap == 3
read = Sequence(name='seq', sequence='AAAACCCCCTTTT')
trimmed = linked_adapter.match_to(read.sequence).trimmed(read)
assert trimmed.name == 'seq'
assert trimmed.sequence == 'CCCCC'
def test_indexed_suffix_adapters_incorrect_type():
with pytest.raises(ValueError):
IndexedSuffixAdapters([
SuffixAdapter("GAAC", indels=False),
PrefixAdapter("TGCT", indels=False),
])
def test_prefix_match_with_n_wildcard_in_read():
adapter = PrefixAdapter("NNNACGT", indels=False)
match = adapter.match_to("TTTACGTAAAA")
assert match is not None and (0, 7) == (match.rstart, match.rstop)
match = adapter.match_to("NTTACGTAAAA")
assert match is not None and (0, 7) == (match.rstart, match.rstop)
def test_indexed_very_similar(caplog):
IndexedPrefixAdapters([
PrefixAdapter("GAAC", max_errors=1, indels=False),
PrefixAdapter("GAAG", max_errors=1, indels=False),
])
assert "cannot be assigned uniquely" in caplog.text
def test_multi_suffix_adapter_incorrect_type():
with pytest.raises(ValueError):
MultiSuffixAdapter([
SuffixAdapter("GAAC", indels=False),
PrefixAdapter("TGCT", indels=False),
])
