How to use the cutadapt.parser.AdapterParser function in cutadapt

def test_linked_adapter_front_required_optional(r1, r2, exp1, exp2):
    # -g X...Y
    a = AdapterParser()._parse("ACG" + r1 + "...TGT" + r2, "front")
    assert isinstance(a, LinkedAdapter)
    assert a.front_required is exp1
    assert a.back_required is exp2

def test_parse_with_parameters():
    parser = AdapterParser(
        max_error_rate=0.2, min_overlap=4, read_wildcards=False,
        adapter_wildcards=False, indels=False)
    a = parser._parse('ACGTACGT; e=0.15', 'front')
    assert a.max_error_rate == 0.15
    assert a.min_overlap == 4

    a = parser._parse('ACGTAAAA; o=5; e=0.11', 'back')
    assert a.max_error_rate == 0.11
    assert a.min_overlap == 5

    for spec in ('thename=ACG;e=0.15 ... TGT;e=0.17', 'thename=ACG;e=0.15...TGT;e=0.17'):
        a = parser._parse(spec, 'back')
        assert isinstance(a, LinkedAdapter)
        assert a.front_adapter.max_error_rate == 0.15
        assert a.back_adapter.max_error_rate == 0.17

def test_anywhere_parameter_back():
    parser = AdapterParser(max_error_rate=0.2, min_overlap=4, read_wildcards=False,
        adapter_wildcards=False, indels=True)
    adapter = list(parser.parse('CTGAAGTGAAGTACACGGTT;anywhere', 'back'))[0]
    assert isinstance(adapter, BackAdapter)
    assert adapter._force_anywhere

    # TODO move the rest to a separate test
    read = Sequence('foo1', 'TGAAGTACACGGTTAAAAAAAAAA')
    from cutadapt.modifiers import AdapterCutter
    cutter = AdapterCutter([adapter])
    trimmed_read = cutter(read, ModificationInfo(read))
    assert trimmed_read.sequence == ''

def test_anchoring_makes_front_linked_adapter_required(seq, req1, req2):
    # -a X...Y
    a = AdapterParser()._parse(seq, "back")
    assert isinstance(a, LinkedAdapter)
    assert a.front_required is req1
    assert a.back_required is req2

def test_linked_adapter_back_required_optional(r1, r2, req1, req2):
    # -a X...Y
    a = AdapterParser()._parse("ACG" + r1 + "...TGT" + r2, "back")
    assert isinstance(a, LinkedAdapter)
    assert a.front_required is req1
    assert a.back_required is req2

def test_parse_file_notation(tmpdir):
    tmp_path = str(tmpdir.join('adapters.fasta'))
    with open(tmp_path, 'w') as f:
        f.write(dedent(""">first_name
            ADAPTER1
            >second_name
            ADAPTER2
            """))
    parser = AdapterParser(
        max_error_rate=0.2, min_overlap=4, read_wildcards=False,
        adapter_wildcards=False, indels=False)

    adapters = list(parser.parse('file:' + tmp_path, cmdline_type='back'))
    assert len(adapters) == 2
    assert adapters[0].name == 'first_name'
    assert adapters[0].sequence == 'ADAPTER1'
    assert adapters[1].name == 'second_name'
    assert adapters[1].sequence == 'ADAPTER2'
    for a in adapters:
        assert a.max_error_rate == 0.2
        assert a.min_overlap == 4
        assert not a.read_wildcards
        assert not a.adapter_wildcards
        assert not a.indels

def test_anywhere_parameter_front():
    parser = AdapterParser(max_error_rate=0.2, min_overlap=4, read_wildcards=False,
        adapter_wildcards=False, indels=True)
    adapter = list(parser.parse('CTGAAGTGAAGTACACGGTT;anywhere', 'front'))[0]
    assert isinstance(adapter, FrontAdapter)
    assert adapter._force_anywhere

    # TODO move the rest to a separate test
    read = Sequence('foo1', 'AAAAAAAAAACTGAAGTGAA')
    from cutadapt.modifiers import AdapterCutter
    cutter = AdapterCutter([adapter])
    trimmed_read = cutter(read, ModificationInfo(read))
    assert trimmed_read.sequence == ''

def adapters_from_args(args) -> Tuple[List[Adapter], List[Adapter]]:
    adapter_parser = AdapterParser(
        max_error_rate=args.error_rate,
        min_overlap=args.overlap,
        read_wildcards=args.match_read_wildcards,
        adapter_wildcards=args.match_adapter_wildcards,
        indels=args.indels,
    )
    try:
        adapters = adapter_parser.parse_multi(args.adapters)
        adapters2 = adapter_parser.parse_multi(args.adapters2)
    except (FileNotFoundError, ValueError) as e:
        raise CommandLineError(e)
    warn_duplicate_adapters(adapters)
    warn_duplicate_adapters(adapters2)
    if args.debug == "trace":
        for adapter in adapters + adapters2:
            adapter.enable_debug()