How to use the cutadapt.modifiers.ModificationInfo function in cutadapt

def test_anywhere_with_errors():
    adapter = AnywhereAdapter("CCGCATTTAG", max_error_rate=0.1)
    for seq, expected_trimmed in (
        ('AACCGGTTccgcatttagGATC', 'AACCGGTT'),
        ('AACCGGTTccgcgtttagGATC', 'AACCGGTT'),  # one mismatch
        ('AACCGGTTccgcatttag', 'AACCGGTT'),
        ('ccgcatttagAACCGGTT', 'AACCGGTT'),
        ('ccgtatttagAACCGGTT', 'AACCGGTT'),  # one mismatch
        ('ccgatttagAACCGGTT', 'AACCGGTT'),  # one deletion
    ):
        read = Sequence('foo', seq)
        cutter = AdapterCutter([adapter], times=1)
        trimmed_read = cutter(read, ModificationInfo(read))
        assert trimmed_read.sequence == expected_trimmed

def test_shortener():
    read = Sequence('read1', 'ACGTTTACGTA', '##456789###')

    shortener = Shortener(0)
    assert shortener(read, ModificationInfo(read)) == Sequence('read1', '', '')

    shortener = Shortener(1)
    assert shortener(read, ModificationInfo(read)) == Sequence('read1', 'A', '#')

    shortener = Shortener(5)
    assert shortener(read, ModificationInfo(read)) == Sequence('read1', 'ACGTT', '##456')

    shortener = Shortener(100)
    assert shortener(read, ModificationInfo(read)) == read

def test_paired_adapter_cutter_actions(action, expected_trimmed1, expected_trimmed2):
    from cutadapt.adapters import BackAdapter
    a1 = BackAdapter("GGTTAA")
    a2 = BackAdapter("AACCGG")
    s1 = Sequence("name", "CCCCGGTTAACCCC")
    s2 = Sequence("name", "TTTTAACCGGTTTT")
    pac = PairedAdapterCutter([a1], [a2], action=action)
    info1 = ModificationInfo(s1)
    info2 = ModificationInfo(s2)
    trimmed1, trimmed2 = pac(s1, s2, info1, info2)
    assert expected_trimmed1 == trimmed1.sequence
    assert expected_trimmed2 == trimmed2.sequence

def test_paired_adapter_cutter_actions(action, expected_trimmed1, expected_trimmed2):
    from cutadapt.adapters import BackAdapter
    a1 = BackAdapter("GGTTAA")
    a2 = BackAdapter("AACCGG")
    s1 = Sequence("name", "CCCCGGTTAACCCC")
    s2 = Sequence("name", "TTTTAACCGGTTTT")
    pac = PairedAdapterCutter([a1], [a2], action=action)
    info1 = ModificationInfo(s1)
    info2 = ModificationInfo(s2)
    trimmed1, trimmed2 = pac(s1, s2, info1, info2)
    assert expected_trimmed1 == trimmed1.sequence
    assert expected_trimmed2 == trimmed2.sequence

"""
    adapter = BackAdapter("TCGATCGATCGAT", max_error_rate=0.1)

    read = Sequence('foo1', 'AAAAAAAAAAATCGTCGATC')
    cutter = AdapterCutter([adapter], times=1)
    trimmed_read = cutter(read, ModificationInfo(read))

    assert trimmed_read.sequence == 'AAAAAAAAAAA'
    assert cutter.adapter_statistics[adapter].back.lengths == {9: 1}
    # We see 1 error at length 9 even though the number of allowed mismatches at
    # length 9 is 0.
    assert cutter.adapter_statistics[adapter].back.errors[9][1] == 1

    read = Sequence('foo2', 'AAAAAAAAAAATCGAACGA')
    cutter = AdapterCutter([adapter], times=1)
    trimmed_read = cutter(read, ModificationInfo(read))

    assert trimmed_read.sequence == read.sequence
    assert cutter.adapter_statistics[adapter].back.lengths == {}

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 test_quality_trimmer():
    read = Sequence('read1', 'ACGTTTACGTA', '##456789###')

    qt = QualityTrimmer(10, 10, 33)
    assert qt(read, ModificationInfo(read)) == Sequence('read1', 'GTTTAC', '456789')

    qt = QualityTrimmer(0, 10, 33)
    assert qt(read, ModificationInfo(read)) == Sequence('read1', 'ACGTTTAC', '##456789')

    qt = QualityTrimmer(10, 0, 33)
    assert qt(read, ModificationInfo(read)) == Sequence('read1', 'GTTTACGTA', '456789###')

def test_statistics():
    read = Sequence('name', 'AAAACCCCAAAA')
    adapters = [BackAdapter("CCCC", max_error_rate=0.1)]
    cutter = AdapterCutter(adapters, times=3)
    cutter(read, ModificationInfo(read))
    # TODO make this a lot simpler
    trimmed_bp = 0
    for adapter in adapters:
        for d in (cutter.adapter_statistics[adapter].front.lengths,
                cutter.adapter_statistics[adapter].back.lengths):
            trimmed_bp += sum(seqlen * count for (seqlen, count) in d.items())
    assert trimmed_bp <= len(read), trimmed_bp

def test_nend_trimmer():
    trimmer = NEndTrimmer()
    seqs = ['NNNNAAACCTTGGNNN', 'NNNNAAACNNNCTTGGNNN', 'NNNNNN']
    trims = ['AAACCTTGG', 'AAACNNNCTTGG', '']
    for seq, trimmed in zip(seqs, trims):
        _seq = Sequence('read1', seq, qualities='#'*len(seq))
        _trimmed = Sequence('read1', trimmed, qualities='#'*len(trimmed))
        assert trimmer(_seq, ModificationInfo(_seq)) == _trimmed

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 == ''