Python MinHash.add_hash方法代码示例

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
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

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
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

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
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)

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
def test_mh_count_common(track_abundance):
    a = MinHash(20, 10, track_abundance=track_abundance)
    for i in range(0, 40, 2):
        a.add_hash(i)

    b = MinHash(20, 10, track_abundance=track_abundance)
    for i in range(0, 80, 4):
        b.add_hash(i)

    assert a.count_common(b) == 10
    assert b.count_common(a) == 10

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
def test_mh_subtract(track_abundance):
    # test subtracting two identically configured minhashes
    a = MinHash(20, 10, track_abundance=track_abundance)
    for i in range(0, 40, 2):
        a.add_hash(i)

    b = MinHash(20, 10, track_abundance=track_abundance)
    for i in range(0, 80, 4):
        b.add_hash(i)

    assert a.subtract_mins(b) == set(range(2, 40, 4))

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
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)

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
def test_mh_merge_check_length(track_abundance):
    a = MinHash(20, 10, track_abundance=track_abundance)
    for i in range(0, 40, 2):
        a.add_hash(i)

    b = MinHash(20, 10, track_abundance=track_abundance)
    for i in range(0, 80, 4):
        b.add_hash(i)

    c = a.merge(b)
    assert(len(c.get_mins()) == 20)

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
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()))

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
def test_minhash_abund_merge_flat_2():
    # this targets a segfault caused by trying to merge
    # a signature with abundance and a signature without abundance.

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

    for i in range(0, 10, 2):
        a.add_hash(i)

    for j in range(0, 10, 3):
        b.add_hash(i)

    a.merge(b)

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
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

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
def test_add_many(track_abundance):
    a = MinHash(0, 10, track_abundance=track_abundance, max_hash=5000)
    b = MinHash(0, 10, track_abundance=track_abundance, max_hash=5000)

    a.add_many(list(range(0, 100, 2)))
    a.add_many(list(range(0, 100, 2)))

    assert len(a) == 50
    assert all(c % 2 == 0 for c in a.get_mins())

    for h in range(0, 100, 2):
        b.add_hash(h)
        b.add_hash(h)

    assert len(b) == 50
    assert a == b

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
def test_minhash_abund_merge_flat():
    # this targets a segfault caused by trying to compute similarity
    # of a signature with abundance and a signature without abundance.
    # the correct behavior for now is to calculate simple Jaccard,
    # i.e. 'flatten' both of them.
    a = MinHash(0, 10, track_abundance=True, max_hash=5000)
    b = MinHash(0, 10, max_hash=5000)

    for i in range(0, 10, 2):
        a.add_hash(i)

    for j in range(0, 10, 3):
        b.add_hash(i)

    # these crashed, previously.
    assert a.similarity(b) == 0.2
    assert b.similarity(a) == 0.2

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
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

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
def test_mh_merge(track_abundance):
    # test merging two identically configured minhashes
    a = MinHash(20, 10, track_abundance=track_abundance)
    for i in range(0, 40, 2):
        a.add_hash(i)

    b = MinHash(20, 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(c) == len(d)
    assert c.get_mins() == d.get_mins()
    assert c.compare(d) == 1.0
    assert d.compare(c) == 1.0

# 需要导入模块: from sourmash._minhash import MinHash [as 别名]
# 或者: from sourmash._minhash.MinHash import add_hash [as 别名]
def test_max_hash(track_abundance):
    # test behavior with max_hash
    mh = MinHash(0, 4, track_abundance=track_abundance, max_hash=35)
    mh.add_hash(10)
    mh.add_hash(20)
    mh.add_hash(30)
    assert mh.get_mins() == [10, 20, 30]
    mh.add_hash(40)
    assert mh.get_mins() == [10, 20, 30]
    mh.add_hash(36)
    assert mh.get_mins() == [10, 20, 30]