def test_cs_5p():
read = ColorspaceSequence("name", b"0123", b"DEFG", b"T")
adapter = ColorspaceAdapter(b"CG", PREFIX, 0.1)
cutter = RepeatedAdapterCutter([adapter])
matches = cutter.find_match(read)
def test_color():
ColorspaceAdapter('0123', where=FRONT, max_error_rate=0.1)
def test_str():
a = Adapter('ACGT', where=BACK, max_error_rate=0.1)
str(a)
str(a.match_to(Sequence(name='seq', sequence='TTACGT')))
ca = ColorspaceAdapter('0123', where=BACK, max_error_rate=0.1)
str(ca)
def test_cs_5p():
read = ColorspaceSequence("name", "0123", "DEFG", "T")
adapter = ColorspaceAdapter("CG", PREFIX, 0.1)
cutter = AdapterCutter([adapter])
trimmed_read = cutter(read)
def test_color():
with pytest.raises(ValueError):
ColorspaceAdapter('0123', where=FRONT, max_error_rate=0.1)
def test_cs_5p():
read = ColorspaceSequence("name", "0123", "DEFG", "T")
adapter = ColorspaceAdapter("CG", PREFIX, 0.1)
cutter = AdapterCutter([adapter])
matches = cutter.find_matches(read)