How to use the cutadapt.adapters.PrefixAdapter function in cutadapt

To help you get started, we’ve selected a few cutadapt examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github marcelm / cutadapt / tests / test_adapters.py View on Github external
def test_multi_prefix_adapter_incorrect_type():
    with pytest.raises(ValueError):
        MultiPrefixAdapter([
            PrefixAdapter("GAAC", indels=False),
            SuffixAdapter("TGCT", indels=False),
        ])
github marcelm / cutadapt / tests / test_adapters.py View on Github external
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'
github marcelm / cutadapt / tests / test_adapters.py View on Github external
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]
github marcelm / cutadapt / tests / test_adapters.py View on Github external
def test_multi_suffix_adapter_incorrect_type():
    with pytest.raises(ValueError):
        MultiSuffixAdapter([
            SuffixAdapter("GAAC", indels=False),
            PrefixAdapter("TGCT", indels=False),
        ])
github marcelm / cutadapt / tests / test_adapters.py View on Github external
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]
github marcelm / cutadapt / tests / test_adapters.py View on Github external
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)