Python MinHash.get_mins方法代碼示例

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
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]

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
def test_basic_dna_bad_force(track_abundance):
    # test behavior on bad DNA; use 100 so multiple hashes get added.
    mh = MinHash(100, 4, track_abundance=track_abundance)
    assert len(mh.get_mins()) == 0
    mh.add_sequence('ATGN', True)     # ambiguous kmer skipped.
    assert len(mh.get_mins()) == 0
    mh.add_sequence('AATGN', True)    # but good k-mers still used.
    assert len(mh.get_mins()) == 1
    mh.add_sequence('AATG', True)     # checking that right kmer was added
    assert len(mh.get_mins()) == 1    # (only 1 hash <- this is a dup)

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
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}

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
def test_basic_dna_bad_force_2(track_abundance):
    # test behavior on bad DNA
    mh = MinHash(100, 4, track_abundance=track_abundance)
    assert len(mh.get_mins()) == 0
    mh.add_sequence('AAGNCGG', True)     # ambiguous kmers skipped.
    assert len(mh.get_mins()) == 0
    mh.add_sequence('AATGNGCGG', True)  # ambiguous kmers skipped.
    assert len(mh.get_mins()) == 2
    mh.add_sequence('AATG', True)        # checking that right kmers were added
    mh.add_sequence('GCGG', True)
    assert len(mh.get_mins()) == 2       # (only 2 hashes should be there)

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
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]

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
def test_basic_dna(track_abundance):
    # verify that MHs of size 1 stay size 1, & act properly as bottom sketches.
    mh = MinHash(1, 4, track_abundance=track_abundance)
    mh.add_sequence('ATGC')
    a = mh.get_mins()

    mh.add_sequence('GCAT')             # this will not get added; hash > ATGC
    b = mh.get_mins()

    print(a, b)
    assert a == b
    assert len(b) == 1

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
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()))

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
def test_bytes_dna(track_abundance):
    mh = MinHash(1, 4, track_abundance=track_abundance)
    mh.add_sequence('ATGC')
    mh.add_sequence(b'ATGC')
    mh.add_sequence(u'ATGC')
    a = mh.get_mins()

    mh.add_sequence('GCAT')             # this will not get added; hash > ATGC
    mh.add_sequence(b'GCAT')             # this will not get added; hash > ATGC
    mh.add_sequence(u'GCAT')             # this will not get added; hash > ATGC
    b = mh.get_mins()

    print(a, b)
    assert a == b
    assert len(b) == 1

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
def test_scaled(track_abundance):
    # test behavior with scaled (alt to max_hash)
    scaled = get_scaled_for_max_hash(35)
    print('XX', scaled, get_max_hash_for_scaled(scaled))
    mh = MinHash(0, 4, track_abundance=track_abundance, scaled=scaled)
    assert mh.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]

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
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

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
def test_abundance_count_common():
    a = MinHash(20, 5, False, track_abundance=True)
    b = MinHash(20, 5, False, track_abundance=False)

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

    b.add_sequence('AAAAA')
    b.add_sequence('GGGGG')
    assert a.count_common(b) == 1
    assert a.count_common(b) == b.count_common(a)

    assert b.get_mins(with_abundance=True) == [2110480117637990133,
                                               10798773792509008305]

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
def test_bytes_protein(track_abundance):
    # verify that we can hash protein/aa sequences
    mh = MinHash(10, 6, True, track_abundance=track_abundance)
    mh.add_protein('AGYYG')
    mh.add_protein(u'AGYYG')
    mh.add_protein(b'AGYYG')

    assert len(mh.get_mins()) == 4

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
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

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
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

# 需要導入模塊: from sourmash._minhash import MinHash [as 別名]
# 或者: from sourmash._minhash.MinHash import get_mins [as 別名]
def test_remove_many(track_abundance):
    a = MinHash(0, 10, track_abundance=track_abundance, max_hash=5000)

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

    orig_sig = signature.SourmashSignature(a)
    orig_md5 = orig_sig.md5sum()

    a.remove_many(list(range(0, 100, 3)))
    new_sig = signature.SourmashSignature(a)
    new_md5 = new_sig.md5sum()

    assert orig_md5 == "f1cc295157374f5c07cfca5f867188a1"
    assert new_md5 == "dd93fa319ef57f4a019c59ee1a8c73e2"
    assert orig_md5 != new_md5

    assert len(a) == 33
    assert all(c % 6 != 0 for c in a.get_mins())