def test_linked_matches_property():
"""Accessing matches property of non-anchored linked adapters"""
# Issue #265
front_adapter = FrontAdapter("GGG")
back_adapter = BackAdapter("TTT")
la = LinkedAdapter(front_adapter, back_adapter, front_required=False, back_required=False, name='name')
assert la.match_to("AAAATTTT").matches == 3
def test_linked_adapter():
linked_adapter = LinkedAdapter('AAAA', 'TTTT')
sequence = Sequence(name='seq', sequence='AAAACCCCCTTTT')
match = linked_adapter.match_to(sequence)
trimmed = linked_adapter.trimmed(match)
assert trimmed.name == 'seq'
assert trimmed.sequence == 'CCCCC'
def test_linked_adapter():
linked_adapter = LinkedAdapter('AAAA', 'TTTT')
sequence = Sequence(name='seq', sequence='AAAACCCCCTTTT')
match = linked_adapter.match_to(sequence)
trimmed = linked_adapter.trimmed(match)
assert trimmed.name == 'seq'
assert trimmed.sequence == 'CCCCC'
def test_issue_265():
"""Crash when accessing the matches property of non-anchored linked adapters"""
s = Sequence('name', 'AAAATTTT')
front_adapter = Adapter('GGG', where=Where.FRONT)
back_adapter = Adapter('TTT', where=Where.BACK)
la = LinkedAdapter(front_adapter, back_adapter, front_required=False, back_required=False, name='name')
assert la.match_to(s).matches == 3
def test_issue_265():
"""Crash when accessing the matches property of non-anchored linked adapters"""
s = Sequence('name', 'AAAATTTT')
front_adapter = SingleAdapter('GGG', where=Where.FRONT)
back_adapter = SingleAdapter('TTT', where=Where.BACK)
la = LinkedAdapter(front_adapter, back_adapter, front_required=False, back_required=False, name='name')
assert la.match_to(s).matches == 3
def test_issue_265():
"""Crash when accessing the matches property of non-anchored linked adapters"""
s = Sequence('name', 'AAAATTTT')
la = LinkedAdapter('GGG',
'TTT',
front_restriction=None,
back_restriction=None)
assert la.match_to(s).matches == 3
def test_linked_adapter():
linked_adapter = LinkedAdapter('AAAA', 'TTTT', min_overlap=4)
assert linked_adapter.front_adapter.min_overlap == 4
assert linked_adapter.back_adapter.min_overlap == 4
sequence = Sequence(name='seq', sequence='AAAACCCCCTTTT')
trimmed = linked_adapter.match_to(sequence).trimmed()
assert trimmed.name == 'seq'
assert trimmed.sequence == 'CCCCC'
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_linked_adapter():
front_adapter = Adapter('AAAA', where=Where.PREFIX, min_overlap=4)
back_adapter = Adapter('TTTT', where=Where.BACK, 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
sequence = Sequence(name='seq', sequence='AAAACCCCCTTTT')
trimmed = linked_adapter.match_to(sequence).trimmed()
assert trimmed.name == 'seq'
assert trimmed.sequence == 'CCCCC'
def test_linked_adapter():
front_adapter = SingleAdapter('AAAA', where=Where.PREFIX, min_overlap=4)
back_adapter = SingleAdapter('TTTT', where=Where.BACK, 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
sequence = Sequence(name='seq', sequence='AAAACCCCCTTTT')
trimmed = linked_adapter.match_to(sequence).trimmed()
assert trimmed.name == 'seq'
assert trimmed.sequence == 'CCCCC'
def test_linked_action_retain(s, expected):
front = FrontAdapter("GGTTAACC")
back = BackAdapter("AACCGG")
adapters: List[Adapter] = [
LinkedAdapter(front,
back,
front_required=False,
back_required=False,
name="linked")
]
ac = AdapterCutter(adapters, action="retain")
seq = Sequence("r1", s)
info = ModificationInfo(seq)
trimmed = ac(seq, info)
assert expected == trimmed.sequence