Python _minhash.MinHash類代碼示例

def test_set_abundance():
    a = MinHash(20, 10, track_abundance=False)

    with pytest.raises(RuntimeError) as e:
        a.set_abundances({1: 3, 2: 4})

    assert "track_abundance=True when constructing" in e.value.args[0]

def test_mh_asymmetric_merge(track_abundance):
    # test merging two asymmetric (different size) MHs
    a = MinHash(20, 10, track_abundance=track_abundance)
    for i in range(0, 40, 2):
        a.add_hash(i)

    # different size: 10
    b = MinHash(10, 10, track_abundance=track_abundance)
    for i in range(0, 80, 4):
        b.add_hash(i)

    c = a.merge(b)
    d = b.merge(a)

    assert len(a) == 20
    assert len(b) == 10
    assert len(c) == len(a)
    assert len(d) == len(b)

    # can't compare different sizes without downsampling
    with pytest.raises(TypeError):
        d.compare(a)

    a = a.downsample_n(d.num)
    print(a.get_mins())
    print(d.get_mins())
    assert d.compare(a) == 1.0

    c = c.downsample_n(b.num)
    assert c.compare(b) == 1.0

def test_no_downsample_scaled_if_n(track_abundance):
    # make sure you can't set max_n and then downsample scaled
    mh = MinHash(2, 4, track_abundance=track_abundance)
    with pytest.raises(ValueError) as excinfo:
        mh.downsample_scaled(100000000)

    assert 'cannot downsample a standard MinHash' in str(excinfo)

def test_div_zero_contained(track_abundance):
    # verify that empty MHs do not yield divide by zero errors for contained_by
    mh = MinHash(1, 4, track_abundance=track_abundance)
    mh2 = mh.copy_and_clear()

    mh.add_sequence('ATGC')
    assert mh.contained_by(mh2) == 0
    assert mh2.contained_by(mh) == 0

def test_basic_dna_bad(track_abundance):
    # test behavior on bad DNA
    mh = MinHash(1, 4, track_abundance=track_abundance)

    with pytest.raises(ValueError) as e:
        mh.add_sequence('ATGR')
    print(e)

    assert 'invalid DNA character in input k-mer: ATGR' in str(e)

def test_reviving_minhash():
    # simulate reading a MinHash from disk
    mh = MinHash(0, 21, max_hash=184467440737095520, seed=42,
                 track_abundance=False)
    mins = (28945103950853965, 74690756200987412, 82962372765557409,
            93503551367950366, 106923350319729608, 135116761470196737,
            160165359281648267, 162390811417732001, 177939655451276972)

    for m in mins:
        mh.add_hash(m)

def test_mh_inplace_concat_asymmetric(track_abundance):
    # test merging two asymmetric (different size) MHs
    a = MinHash(20, 10, track_abundance=track_abundance)
    for i in range(0, 40, 2):
        a.add_hash(i)

    # different size: 10
    b = MinHash(10, 10, track_abundance=track_abundance)
    for i in range(0, 80, 4):
        b.add_hash(i)

    c = a.__copy__()
    c += b

    d = b.__copy__()
    d += a

    assert len(a) == 20
    assert len(b) == 10
    assert len(c) == len(a)
    assert len(d) == len(b)

    try:
        d.compare(a)
    except TypeError as exc:
        assert 'must have same num' in str(exc)

    a = a.downsample_n(d.num)
    assert d.compare(a) == 1.0 # see: d += a, above.

    c = c.downsample_n(b.num)
    assert c.compare(b) == 0.5

def test_minhash_abund_capacity_increase():
    # this targets bug #319, a segfault caused by invalidation of
    # std::vector iterators upon vector resizing.

    # this should set capacity to 1000 - see KmerMinHash constructor call
    # to 'reserve' when n > 0 for specific parameter.
    a = MinHash(0, 10, track_abundance=True, max_hash=5000)

    # 1001 is dependent on the value passed to reserve (currently 1000).
    for i in range(1001, 0, -1):
        a.add_hash(i)

class TimeMinHashSuite:
    def setup(self):
        self.mh = MinHash(500, 21, track_abundance=False)
        self.sequences = load_sequences(get_test_data('ecoli.genes.fna')) * 10

        self.populated_mh = MinHash(500, 21, track_abundance=False)
        for seq in self.sequences:
            self.populated_mh.add_sequence(seq)

    def time_add_sequence(self):
        mh = self.mh
        sequences = self.sequences
        for seq in sequences:
            mh.add_sequence(seq)

    def time_get_mins(self):
        mh = self.populated_mh
        for i in range(500):
            mh.get_mins()

    def time_add_hash(self):
        mh = self.mh
        for i in range(10000):
            mh.add_hash(i)

    def time_compare(self):
        mh = self.mh
        other_mh = self.populated_mh
        for i in range(500):
            mh.compare(other_mh)

    def time_count_common(self):
        mh = self.mh
        other_mh = self.populated_mh
        for i in range(500):
            mh.count_common(other_mh)

    def time_merge(self):
        mh = self.mh
        other_mh = self.populated_mh
        for i in range(500):
            mh.merge(other_mh)

    def time_copy(self):
        mh = self.populated_mh
        for i in range(500):
            mh.__copy__()

    def time_concat(self):
        mh = self.mh
        other_mh = self.populated_mh
        for i in range(500):
            mh += other_mh

def test_size_limit(track_abundance):
    # test behavior with size limit of 3
    mh = MinHash(3, 4, track_abundance=track_abundance)
    mh.add_hash(10)
    mh.add_hash(20)
    mh.add_hash(30)
    assert mh.get_mins() == [10, 20, 30]
    mh.add_hash(5) # -> should push 30 off end
    assert mh.get_mins() == [5, 10, 20]

def test_minhash_abund_add():
    # this targets part of bug #319, a segfault caused by invalidation of
    # std::vector iterators upon vector resizing - in this case, there
    # was also a bug in inserting into the middle of mins when scaled was set.

    a = MinHash(0, 10, track_abundance=True, max_hash=5000)

    n = 0
    for i in range(10, 0, -1):
        a.add_hash(i)
        n += 1
        assert len(a.get_mins()) == n
        print(len(a.get_mins()))

def test_abundance_simple():
    a = MinHash(20, 5, False, track_abundance=True)

    a.add_sequence('AAAAA')
    assert a.get_mins() == [2110480117637990133]
    assert a.get_mins(with_abundance=True) == {2110480117637990133: 1}

    a.add_sequence('AAAAA')
    assert a.get_mins() == [2110480117637990133]
    assert a.get_mins(with_abundance=True) == {2110480117637990133: 2}

def test_consume_lowercase(track_abundance):
    a = MinHash(20, 10, track_abundance=track_abundance)
    b = MinHash(20, 10, track_abundance=track_abundance)

    a.add_sequence('TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGA'.lower())
    b.add_sequence('TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGA')

    assert a.compare(b) == 1.0
    assert b.compare(b) == 1.0
    assert b.compare(a) == 1.0
    assert a.compare(a) == 1.0

def test_mh_copy_and_clear_with_max_hash(track_abundance):
    # test basic creation of new, empty MinHash w/max_hash param set
    a = MinHash(0, 10, track_abundance=track_abundance, max_hash=20)
    for i in range(0, 40, 2):
        a.add_hash(i)

    b = a.copy_and_clear()
    assert a.ksize == b.ksize
    assert b.num == a.num
    assert b.max_hash == 20
    assert not b.is_protein
    assert b.track_abundance == track_abundance
    assert b.seed == a.seed
    assert len(b.get_mins()) == 0
    assert a.scaled == b.scaled
    assert b.scaled != 0

def test_pickle_scaled(track_abundance):
    a = MinHash(0, 10, track_abundance=track_abundance, scaled=922337203685477632)
    for i in range(0, 40, 2):
        a.add_hash(i)

    b = pickle.loads(pickle.dumps(a))
    assert a.ksize == b.ksize
    assert b.num == a.num
    assert b.max_hash == a.max_hash
    assert b.max_hash == 20
    assert not b.is_protein
    assert b.track_abundance == track_abundance
    assert b.seed == a.seed
    assert len(b.get_mins()) == len(a.get_mins())
    assert len(b.get_mins()) == 11
    assert a.scaled == b.scaled
    assert b.scaled != 0