test__minhash.py

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# Contact: titus@idyll.org
# pylint: disable=missing-docstring,protected-access

import itertools
import pickle
import math

import pytest

import sourmash
from sourmash.minhash import (
    MinHash,
    hash_murmur,
    _get_scaled_for_max_hash,
    _get_max_hash_for_scaled,
    translate_codon
)
from sourmash import signature

from . import sourmash_tst_utils as utils

# add:
# * get default params from Python
# * keyword args for minhash constructor
# * trap error from handing protein/non-DNA to a DNA MH
# * fail on untagged/unloaded countgraph
# * nan on empty minhash
# * define equals

scaled50 = _get_scaled_for_max_hash(50)
scaled100 = _get_scaled_for_max_hash(100)
scaled5000 = _get_scaled_for_max_hash(5000)


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)
    assert mh.moltype == 'DNA'

    mh.add_sequence('ATGC')
    a = mh.hashes

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

    print(a, b)
    assert list(a) == list(b)
    assert len(b) == 1
    assert list(a)[0] == list(b)[0] == 12415348535738636339


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

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


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_bytes_dna(track_abundance):
    mh = MinHash(1, 4, track_abundance=track_abundance)
    mh.add_sequence('ATGC')
    mh.add_sequence(b'ATGC')
    mh.add_sequence('ATGC')
    a = mh.hashes

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

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


def test_bytes_protein_dayhoff(track_abundance, dayhoff):
    # verify that we can hash protein/aa sequences
    mh = MinHash(10, 6, True, dayhoff=dayhoff, hp=False,
                 track_abundance=track_abundance)

    expected_moltype = 'protein'
    if dayhoff:
        expected_moltype = 'dayhoff'
    assert mh.moltype == expected_moltype

    mh.add_protein('AGYYG')
    mh.add_protein('AGYYG')
    mh.add_protein(b'AGYYG')

    assert len(mh.hashes) == 4


def test_protein_dayhoff(track_abundance, dayhoff):
    # verify that we can hash protein/aa sequences
    mh = MinHash(10, 6, True, dayhoff=dayhoff, hp=False, track_abundance=track_abundance)
    mh.add_protein('AGYYG')

    assert len(mh.hashes) == 4


def test_bytes_protein_hp(track_abundance, hp):
    # verify that we can hash protein/aa sequences
    mh = MinHash(10, 6, True, dayhoff=False, hp=hp, track_abundance=track_abundance)
    expected_moltype = 'protein'
    if hp:
        expected_moltype = 'hp'
    assert mh.moltype == expected_moltype

    mh.add_protein('AGYYG')
    mh.add_protein(u'AGYYG')
    mh.add_protein(b'AGYYG')

    if hp:
        assert len(mh.hashes) == 1
    else:
        assert len(mh.hashes) == 4


def test_protein_hp(track_abundance, hp):
    # verify that we can hash protein/aa sequences
    mh = MinHash(10, 6, True, dayhoff=False, hp=hp, track_abundance=track_abundance)
    mh.add_protein('AGYYG')

    if hp:
        assert len(mh.hashes) == 1
    else:
        assert len(mh.hashes) == 4


def test_module_translate_codon(track_abundance):
    # Ensure that translation occurs properly - module level function tests
    assert "S" == translate_codon('TCT')
    assert "S" == translate_codon('TC')
    assert "X" == translate_codon("T")

    with pytest.raises(ValueError):
        translate_codon("")
        translate_codon("TCTA")


def test_dayhoff(track_abundance):
    # verify that we can hash to dayhoff-encoded protein/aa sequences
    mh_dayhoff = MinHash(10, 6, is_protein=True,
                         dayhoff=True, hp=False, track_abundance=track_abundance)
    mh_dayhoff.add_sequence('ACTGAC')

    assert len(mh_dayhoff.hashes) == 2
    # verify that dayhoff-encoded hashes are different from protein/aa hashes
    mh_protein = MinHash(10, 6, is_protein=True, track_abundance=track_abundance)
    mh_protein.add_sequence('ACTGAC')

    assert len(mh_protein.hashes) == 2
    print(mh_protein.hashes)
    print(mh_dayhoff.hashes)
    assert mh_protein.hashes != mh_dayhoff.hashes


def test_hp(track_abundance):
    # verify that we can hash to hp-encoded protein/aa sequences
    mh_hp = MinHash(10, 6, is_protein=True,
                    dayhoff=False, hp=True, track_abundance=track_abundance)
    assert mh_hp.moltype == 'hp'

    mh_hp.add_sequence('ACTGAC')

    assert len(mh_hp.hashes) == 2
    # verify that hp-encoded hashes are different from protein/aa hashes
    mh_protein = MinHash(10, 6, is_protein=True, track_abundance=track_abundance)
    mh_protein.add_sequence('ACTGAC')

    assert len(mh_protein.hashes) == 2
    assert mh_protein.hashes != mh_hp.hashes


def test_protein_short(track_abundance):
    # verify that we can hash protein/aa sequences
    mh = MinHash(10, 9, True, track_abundance=track_abundance)
    mh.add_protein('AG')

    assert len(mh.hashes) == 0, mh.hashes


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 list(sorted(mh.hashes)) == [10, 20, 30]
    mh.add_hash(5) # -> should push 30 off end
    assert list(sorted(mh.hashes)) == [5, 10, 20]


def test_scaled(track_abundance):
    # test behavior with scaled
    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 list(sorted(mh.hashes)) == [10, 20, 30]
    mh.add_hash(40)
    assert list(sorted(mh.hashes)) == [10, 20, 30]
    mh.add_hash(36)
    assert list(sorted(mh.hashes)) == [10, 20, 30]


def test_no_scaled(track_abundance):
    # no 'scaled', num=0 - should fail
    with pytest.raises(ValueError):
        mh = MinHash(0, 4, track_abundance=track_abundance)


def test_max_hash_conversion():
    SCALED=100000
    max_hash = _get_max_hash_for_scaled(SCALED)
    new_scaled = _get_scaled_for_max_hash(max_hash)
    assert new_scaled == SCALED


def test_max_hash_and_scaled_zero():
    max_hash = _get_max_hash_for_scaled(0)
    new_scaled = _get_scaled_for_max_hash(0)
    assert max_hash == new_scaled
    assert max_hash == 0


def test_max_hash_and_scaled_error(track_abundance):
    # test behavior when supplying both max_hash and scaled
    with pytest.raises(ValueError):
        mh = MinHash(0, 4, track_abundance=track_abundance, max_hash=35,
                     scaled=5)


def test_max_hash_cannot_limit(track_abundance):
    # make sure you can't set both n and scaled.
    with pytest.raises(ValueError):
        mh = MinHash(2, 4, track_abundance=track_abundance,
                     scaled=_get_scaled_for_max_hash(1))


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.value)


def test_scaled_num_both(track_abundance):
    # make sure you can't set both max_n and scaled.
    with pytest.raises(ValueError):
        mh = MinHash(2, 4, track_abundance=track_abundance, scaled=2)


def test_mh_jaccard_similarity():
    # check actual Jaccard value for a non-trivial case
    a = MinHash(0, 20, scaled=scaled50, track_abundance=False)
    b = MinHash(0, 20, scaled=scaled50, track_abundance=False)
    a.add_many([1, 3, 5, 8])
    b.add_many([1, 3, 5, 6, 8, 10])

    assert a.similarity(b) == 4. / 6.


def test_mh_similarity_downsample_jaccard_value():
    # check jaccard value after downsampling

    # max_hash = 50
    a = MinHash(0, 20, scaled=scaled50, track_abundance=False)
    # max_hash = 100
    b = MinHash(0, 20, scaled=scaled100, track_abundance=False)

    a.add_many([1, 3, 5, 8, 70])
    b.add_many([1, 3, 5, 6, 8, 10, 70 ])

    # the hash=70 will be truncated by downsampling
    assert a.similarity(b, downsample=True) == 4. / 6.


def test_mh_angular_similarity():
    # check actual angular similarity for a non-trivial case, taken from:
    # https://www.sciencedirect.com/topics/computer-science/cosine-similarity
    # note: angular similarity is 1 - 2*(acos(sim) / pi), when elements
    # are always positive (https://en.wikipedia.org/wiki/Cosine_similarity)
    a = MinHash(0, 20, scaled=scaled50, track_abundance=True)
    b = MinHash(0, 20, scaled=scaled50, track_abundance=True)
    a.set_abundances({ 1:5, 3:3, 5:2, 8:2})
    b.set_abundances({ 1:3, 3:2, 5:1, 6:1, 8:1, 10:1 })

    cos_sim = 0.9356
    angular_sim = 1 - 2*math.acos(cos_sim) / math.pi
    assert round(angular_sim, 4) == 0.7703

    assert round(a.similarity(b), 4) == round(angular_sim, 4)


def test_mh_angular_similarity_2():
    # check actual angular similarity for a second non-trivial case
    a = MinHash(0, 20, scaled=scaled100, track_abundance=True)
    b = MinHash(0, 20, scaled=scaled100, track_abundance=True)
    a.set_abundances({ 1:5, 3:3, 5:2, 8:2, 70:70 })
    b.set_abundances({ 1:3, 3:2, 5:1, 6:1, 8:1, 10:1, 70:70 })

    assert round(a.similarity(b), 4) == 0.9728

    # ignore_abundance => jaccard
    assert a.similarity(b, ignore_abundance=True) == 5. / 7.


def test_mh_similarity_downsample_angular_value():
    # test downsample=True argument to MinHash.similarity

    # max_hash = 50
    a = MinHash(0, 20, scaled=scaled50, track_abundance=True)
    # max_hash = 100
    b = MinHash(0, 20, scaled=scaled100, track_abundance=True)

    a.set_abundances({ 1:5, 3:3, 5:2, 8:2, 70:70 })
    b.set_abundances({ 1:3, 3:2, 5:1, 6:1, 8:1, 10:1, 70:70 })

    # the hash=70 will be truncated by downsampling
    sim = a.similarity(b, downsample=True)
    assert round(sim, 4) == 0.7703

    # with ignore_abundance, will be equal to jaccard
    jaccard = a.similarity(b, downsample=True, ignore_abundance=True)
    assert jaccard == 4. / 6.


def test_mh_similarity_downsample_true(track_abundance):
    # verify sim(a, b) == sim(b, a), with and without ignore_abundance

    # max_hash = 50
    a = MinHash(0, 20, scaled=scaled50, track_abundance=track_abundance)
    # max_hash = 100
    b = MinHash(0, 20, scaled=scaled100, track_abundance=track_abundance)

    a_values = { 1:5, 3:3, 5:2, 8:2}
    b_values = { 1:3, 3:2, 5:1, 6:1, 8:1, 10:1 }
    if track_abundance:
        a.set_abundances(a_values)
        b.set_abundances(b_values)
    else:
        a.add_many(a_values.keys())
        b.add_many(b_values.keys())

    # downsample=True => no error; values should match either way
    x = a.similarity(b, ignore_abundance=True, downsample=True)
    y = b.similarity(a, ignore_abundance=True, downsample=True)
    assert x == y

    # downsample=True => no error; values should match either way
    x = a.similarity(b, ignore_abundance=False, downsample=True)
    y = b.similarity(a, ignore_abundance=False, downsample=True)
    assert x == y


def test_mh_similarity_downsample_errors(track_abundance):
    # test downsample=False (default) argument to MinHash.similarity

    # max_hash = 50
    a = MinHash(0, 20, scaled=scaled50, track_abundance=track_abundance)
    # max_hash = 100
    b = MinHash(0, 20, scaled=scaled100, track_abundance=track_abundance)

    a_values = { 1:5, 3:3, 5:2, 8:2}
    b_values = { 1:3, 3:2, 5:1, 6:1, 8:1, 10:1 }
    if track_abundance:
        a.set_abundances(a_values)
        b.set_abundances(b_values)
    else:
        a.add_many(a_values.keys())
        b.add_many(b_values.keys())

    # error, incompatible max hash
    with pytest.raises(ValueError) as e:
        a.similarity(b, ignore_abundance=True)   # downsample=False
    assert 'mismatch in scaled; comparison fail' in str(e.value)

    with pytest.raises(ValueError) as e:
        a.similarity(b, ignore_abundance=False)  # downsample=False
    assert 'mismatch in scaled; comparison fail' in str(e.value)

    with pytest.raises(ValueError) as e:
        b.similarity(a, ignore_abundance=True)   # downsample=False
    assert 'mismatch in scaled; comparison fail' in str(e.value)

    with pytest.raises(ValueError) as e:
        b.similarity(a, ignore_abundance=False)  # downsample=false
    assert 'mismatch in scaled; comparison fail' in str(e.value)


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.value)


def test_basic_dna_bad_2(track_abundance):
    # test behavior on bad DNA
    mh = MinHash(1, 6, track_abundance=track_abundance)

    with pytest.raises(ValueError):
        mh.add_protein('YYYY')


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.hashes) == 0
    mh.add_sequence('ATGN', True)     # ambiguous kmer skipped.
    assert len(mh.hashes) == 0
    mh.add_sequence('AATGN', True)    # but good k-mers still used.
    assert len(mh.hashes) == 1
    mh.add_sequence('AATG', True)     # checking that right kmer was added
    assert len(mh.hashes) == 1    # (only 1 hash <- this is a dup)


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.hashes) == 0
    mh.add_sequence('AAGNCGG', True)     # ambiguous kmers skipped.
    assert len(mh.hashes) == 0
    mh.add_sequence('AATGNGCGG', True)  # ambiguous kmers skipped.
    assert len(mh.hashes) == 2
    mh.add_sequence('AATG', True)        # checking that right kmers were added
    mh.add_sequence('GCGG', True)
    assert len(mh.hashes) == 2       # (only 2 hashes should be there)


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 round(a.similarity(b), 3) == 1.0
    assert round(b.similarity(b), 3) == 1.0
    assert round(b.similarity(a), 3) == 1.0
    assert round(a.similarity(a), 3) == 1.0


def test_similarity_1(track_abundance):
    a = MinHash(20, 10, track_abundance=track_abundance)
    b = MinHash(20, 10, track_abundance=track_abundance)

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

    assert round(a.similarity(b), 3) == 1.0
    assert round(b.similarity(b), 3) == 1.0
    assert round(b.similarity(a), 3) == 1.0
    assert round(a.similarity(a), 3) == 1.0

    # add same sequence again
    b.add_sequence('TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGA')
    assert round(a.similarity(b), 3) == 1.0
    assert round(b.similarity(b), 3) == 1.0
    assert round(b.similarity(a), 3) == 1.0
    assert round(a.similarity(a), 3) == 1.0


    b.add_sequence('GATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTT')
    x = a.similarity(b)
    assert x >= 0.3, x

    x = b.similarity(a)
    assert x >= 0.3, x
    assert round(a.similarity(a), 3) == 1.0
    assert round(b.similarity(b), 3) == 1.0


def test_mh_copy(track_abundance):
    a = MinHash(20, 10, track_abundance=track_abundance)

    a.add_sequence('TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGA')
    b = a.__copy__()
    assert round(b.similarity(a), 3) == 1.0


def test_mh_len(track_abundance):
    a = MinHash(20, 10, track_abundance=track_abundance)

    assert len(a) == 20
    a.add_sequence('TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGA')
    assert len(a) == 20


def test_mh_len(track_abundance):
    a = MinHash(20, 10, track_abundance=track_abundance)
    for i in range(0, 40, 2):
        a.add_hash(i)

    assert list(sorted(a.hashes)) == list(range(0, 40, 2))


def test_mh_unsigned_long_long(track_abundance):
    a = MinHash(20, 10, track_abundance=track_abundance)
    a.add_hash(9227159859419181011)        # too big for a C long int.
    assert 9227159859419181011 in a.hashes


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


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

    with pytest.raises(ValueError):
        a.count_common(b)


def test_mh_count_common_diff_maxhash(track_abundance):
    a = MinHash(0, 5, False, track_abundance=track_abundance,
                scaled=_get_scaled_for_max_hash(1))
    b = MinHash(0, 5, True, track_abundance=track_abundance,
                scaled=_get_scaled_for_max_hash(2))

    with pytest.raises(ValueError):
        a.count_common(b)


def test_mh_count_common_diff_seed(track_abundance):
    a = MinHash(20, 5, False, track_abundance=track_abundance, seed=1)
    b = MinHash(20, 5, True, track_abundance=track_abundance, seed=2)

    with pytest.raises(ValueError):
        a.count_common(b)


def test_mh_count_common_diff_ksize(track_abundance):
    a = MinHash(20, 5, track_abundance=track_abundance)
    b = MinHash(20, 6, track_abundance=track_abundance)

    with pytest.raises(ValueError):
        a.count_common(b)


def test_mh_count_common_notmh(track_abundance):
    a = MinHash(20, 5, track_abundance=track_abundance)
    b = set()

    with pytest.raises(TypeError):
        a.count_common(b)


def test_mh_downsample_num_error(track_abundance):
    a = MinHash(20, 10, track_abundance=track_abundance)
    with pytest.raises(ValueError):
        a.downsample(num=30)


def test_mh_jaccard_asymmetric_num(track_abundance):
    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)

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

    # with 'jaccard', this will raise an error b/c different num
    with pytest.raises(TypeError):
        a.jaccard(b)

    a = a.downsample(num=10)
    # CTB note: this used to be 'compare', is now 'jaccard'
    assert a.jaccard(b) == 0.5
    assert b.jaccard(a) == 0.5


def test_mh_merge_typeerror(track_abundance):
    a = MinHash(20, 10, track_abundance=track_abundance)
    with pytest.raises(TypeError):
        a.merge(set())


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 list(sorted(c.hashes)) == list(sorted(d.hashes))

    if track_abundance:
        assert round(c.similarity(d), 3) == 0.91
        assert round(d.similarity(c), 3) == 0.91
    else:
        assert round(c.similarity(d), 3) == 1.0
        assert round(d.similarity(c), 3) == 1.0


def test_mh_merge_empty_num(track_abundance):
    # test merging two identically configured minhashes, one empty
    a = MinHash(20, 10, track_abundance=track_abundance)

    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)
    assert len(c) == len(d)

    assert list(sorted(c.hashes)) == list(sorted(d.hashes))
    assert round(c.similarity(d), 3) == 1.0
    assert round(d.similarity(c), 3) == 1.0


def test_mh_merge_empty_scaled(track_abundance):
    # test merging two identically configured minhashes, one empty
    a = MinHash(0, 10, scaled=1, track_abundance=track_abundance)

    b = MinHash(0, 10, scaled=1, 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)
    assert len(c) == len(d)

    assert list(sorted(c.hashes)) == list(sorted(d.hashes))
    assert round(c.similarity(d), 3) == 1.0
    assert round(d.similarity(c), 3) == 1.0


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.hashes) == 20


def test_mh_merge_check_length2(track_abundance):
    # merged MH doesn't have full number of elements
    a = MinHash(4, 10, track_abundance=track_abundance)
    a.add_hash(3)
    a.add_hash(1)
    a.add_hash(4)

    b = MinHash(4, 10, track_abundance=track_abundance)
    b.add_hash(3)
    b.add_hash(1)
    b.add_hash(4)

    c = a.merge(b)
    assert len(c.hashes) == 3

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 use jaccard on different nums without downsampling
    with pytest.raises(TypeError):
        d.jaccard(a)

    a = a.downsample(num=d.num)

    if track_abundance:
        assert round(d.similarity(a), 3) == 0.91
    else:
        assert round(d.similarity(a), 3) == 1.0

    c = c.downsample(num=b.num)
    if track_abundance:
        assert round(c.similarity(b), 3) == 0.91
    else:
        assert c.similarity(b) == 1.0


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

    a = a.downsample(num=d.num)
    if track_abundance:
        assert round(d.similarity(a), 3) == 0.795 # see: d += a, above.
    else:
        assert d.similarity(a) == 1.0 # see: d += a, above.

    c = c.downsample(num=b.num)
    if track_abundance:
        assert round(c.similarity(b), 3) == 0.436
    else:
        assert c.similarity(b) == 0.5


def test_mh_inplace_concat(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.__copy__()
    c += b
    d = b.__copy__()
    d += a

    assert len(c) == len(d)
    assert c.hashes == d.hashes
    assert round(c.similarity(d), 3) == 1.0
    assert round(d.similarity(c), 3) == 1.0


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

    with pytest.raises(ValueError):
        a.merge(b)


def test_mh_merge_diff_ksize(track_abundance):
    a = MinHash(20, 5, track_abundance=track_abundance)
    b = MinHash(20, 6, track_abundance=track_abundance)

    with pytest.raises(ValueError):
        a.merge(b)


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

    with pytest.raises(ValueError):
        a.similarity(b)


def test_mh_similarity_diff_ksize(track_abundance):
    a = MinHash(20, 5, track_abundance=track_abundance)
    b = MinHash(20, 6, track_abundance=track_abundance)

    with pytest.raises(ValueError):
        a.similarity(b)


def test_mh_similarity_diff_seed(track_abundance):
    a = MinHash(20, 5, track_abundance=track_abundance, seed=1)
    b = MinHash(20, 5, track_abundance=track_abundance, seed=2)

    with pytest.raises(ValueError):
        a.similarity(b)


def test_mh_compare_diff_max_hash(track_abundance):
    a = MinHash(0, 5, track_abundance=track_abundance,
                scaled=_get_max_hash_for_scaled(5))

    b = MinHash(0, 5, track_abundance=track_abundance,
                scaled=_get_max_hash_for_scaled(10))

    with pytest.raises(ValueError):
        a.similarity(b)


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

    with pytest.raises(ValueError):
        a += b


def test_mh_concat_diff_ksize(track_abundance):
    a = MinHash(20, 5, track_abundance=track_abundance)
    b = MinHash(20, 6, track_abundance=track_abundance)

    with pytest.raises(ValueError):
        a += b


def test_mh_concat_diff_max_hash(track_abundance):
    a = MinHash(0, 5, track_abundance=track_abundance,
                scaled=_get_max_hash_for_scaled(5))
    b = MinHash(0, 5, track_abundance=track_abundance,
                scaled=_get_max_hash_for_scaled(10))

    with pytest.raises(ValueError):
        a += b


def test_mh_concat_diff_seed(track_abundance):
    a = MinHash(20, 5, track_abundance=track_abundance, seed=1)
    b = MinHash(20, 5, track_abundance=track_abundance, seed=2)

    with pytest.raises(ValueError):
        a += b


def test_short_sequence(track_abundance):
    a = MinHash(20, 5, track_abundance=track_abundance)
    a.add_sequence('GGGG')
    # adding a short sequence should fail silently
    assert len(a.hashes) == 0


def test_bytes_murmur():
    x = hash_murmur("ACG")
    assert x == 1731421407650554201

    x = hash_murmur(b"ACG")
    assert x == 1731421407650554201

    x = hash_murmur(u"ACG")
    assert x == 1731421407650554201


def test_murmur():
    x = hash_murmur("ACG")
    assert x == 1731421407650554201

    try:
        x = hash_murmur()
        assert 0, "hash_murmur requires an argument"
    except TypeError:
        pass

    x = hash_murmur("ACG", 42)
    assert x == 1731421407650554201

    y = hash_murmur("ACG", 43)
    assert y != x


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

    a.add_sequence('AAAAA')
    assert list(a.hashes) == [2110480117637990133]
    assert a.hashes == {2110480117637990133: 1}

    a.add_sequence('AAAAA')
    assert list(a.hashes) == [2110480117637990133]
    assert a.hashes == {2110480117637990133: 2}


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

    a.add_hash_with_abundance(10, 1)
    assert a.hashes == {10: 1}

    a.add_hash_with_abundance(20, 2)
    assert a.hashes == {10: 1, 20: 2}

    a.add_hash_with_abundance(10, 2)
    assert a.hashes == {10: 3, 20: 2}


def test_add_hash_with_abundance_2():
    a = MinHash(20, 5, False, track_abundance=False)

    with pytest.raises(RuntimeError) as e:
        a.add_hash_with_abundance(10, 1)

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


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

    a.add_hash(10)
    assert a.hashes == {10: 1}

    a.clear()
    assert a.hashes == {}


def test_clear_2():
    a = MinHash(20, 5, False, track_abundance=False)

    a.add_hash(10)
    assert list(a.hashes) == [10]

    a.clear()
    assert list(a.hashes) == []


def test_abundance_simple_2():
    a = MinHash(20, 5, False, track_abundance=True)
    b = MinHash(20, 5, False, track_abundance=True)

    a.add_sequence('AAAAA')
    assert list(a.hashes) == [2110480117637990133]
    assert a.hashes == {2110480117637990133: 1}

    a.add_sequence('AAAAA')
    assert list(a.hashes) == [2110480117637990133]
    assert a.hashes == {2110480117637990133: 2}

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


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 list(a.hashes) == [2110480117637990133]
    assert a.hashes == {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 list(sorted(b.hashes)) == [2110480117637990133, 10798773792509008305]


def test_abundance_similarity():
    a = MinHash(20, 10, track_abundance=True)
    b = MinHash(20, 10, track_abundance=False)

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

    assert round(a.similarity(b), 3) == 1.0
    assert round(b.similarity(b), 3) == 1.0
    assert round(b.similarity(a), 3) == 1.0
    assert round(a.similarity(a), 3) == 1.0

    # add same sequence again
    b.add_sequence('TGCCGCCCAGCACCGGGTGACTAGGTTGAGCCATGATTAACCTGCAATGA')
    assert round(a.similarity(b), 3) == 1.0
    assert round(b.similarity(b), 3) == 1.0
    assert round(b.similarity(a), 3) == 1.0
    assert round(a.similarity(a), 3) == 1.0

    b.add_sequence('GATTGGTGCACACTTAACTGGGTGCCGCGCTGGTGCTGATCCATGAAGTT')
    x = a.similarity(b)
    assert x >= 0.3, x

    x = b.similarity(a)
    assert x >= 0.3, x
    assert round(a.similarity(a), 3) == 1.0
    assert round(b.similarity(b), 3) == 1.0


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_set_abundance_2():
    datapath = utils.get_test_data("genome-s12.fa.gz.sig")
    sig = sourmash.load_one_signature(datapath,
                                      ksize=30,
                                      select_moltype='dna')
    new_mh = sig.minhash.copy_and_clear()
    mins = sig.minhash.hashes
    mins = {k: 1 for k in mins}
    new_mh.track_abundance = True
    new_mh.set_abundances(mins)

    assert set(new_mh.hashes) == set(mins)


def test_set_abundance_clear():
    # on empty minhash, clear should have no effect
    a = MinHash(20, 5, False, track_abundance=True)
    b = MinHash(20, 5, False, track_abundance=True)

    a.set_abundances({1: 3, 2: 4}, clear=True)
    b.set_abundances({1: 3, 2: 4}, clear=False)

    assert list(sorted(a.hashes)) == list(sorted(b.hashes))


def test_set_abundance_clear_2():
    # default should be clear=True
    a = MinHash(20, 5, False, track_abundance=True)

    a.add_hash(10)
    assert a.hashes == {10: 1}

    a.set_abundances({20: 2})
    assert a.hashes == {20: 2}


def test_set_abundance_clear_3():
    a = MinHash(20, 5, False, track_abundance=True)

    a.add_hash(10)
    assert a.hashes == {10: 1}
    
    a.set_abundances({20: 1, 30: 4}, clear=False)
    assert a.hashes == {10: 1, 20: 1, 30: 4}


def test_set_abundance_clear_4():
    # setting the abundance of an already set hash should add
    # the abundances together
    a = MinHash(20, 5, False, track_abundance=True)

    a.set_abundances({20: 2, 10: 1}, clear=False)   # should also sort the hashes
    assert a.hashes == {10: 1, 20: 2}

    a.set_abundances({20: 1, 10: 2}, clear=False)
    assert a.hashes == {10: 3, 20: 3}


def test_reset_abundance_initialized():
    a = MinHash(1, 4, track_abundance=True)
    a.add_sequence('ATGC')

    # If we had a minhash with abundances and drop it, this shouldn't fail.
    # Convert from Abundance to Regular MinHash
    a.track_abundance = False

    assert list(a.hashes) == [12415348535738636339]


def test_set_abundance_initialized():
    a = MinHash(1, 4, track_abundance=False)
    a.add_sequence('ATGC')

    with pytest.raises(RuntimeError) as e:
        a.track_abundance = True

    assert "Can only set track_abundance=True if the MinHash is empty" in e.value.args[0]


def test_set_abundance_num():
    a = MinHash(2, 10, track_abundance=True)

    a.set_abundances({1: 3, 2: 4})

    assert a.hashes == {1: 3, 2: 4}


def test_mh_copy_and_clear(track_abundance):
    # test basic creation of new, empty MinHash
    a = MinHash(20, 10, track_abundance=track_abundance)
    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 == 0
    assert not b.is_protein
    assert b.track_abundance == track_abundance
    assert b.seed == a.seed
    assert len(b.hashes) == 0
    assert a.scaled == b.scaled
    assert b.scaled == 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,
                scaled=_get_scaled_for_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.hashes) == 0
    assert a.scaled == b.scaled
    assert b.scaled != 0


def test_scaled_property(track_abundance):
    scaled = 10000
    a = MinHash(0, 10, track_abundance=track_abundance, scaled=scaled)
    assert a.scaled == scaled


def test_pickle_max_hash(track_abundance):
    a = MinHash(0, 10, track_abundance=track_abundance,
                scaled=_get_scaled_for_max_hash(20))
    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.hashes) == len(a.hashes)
    assert len(b.hashes) == 11
    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.hashes) == len(a.hashes)
    assert len(b.hashes) == 11
    assert a.scaled == b.scaled
    assert b.scaled != 0


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, scaled=scaled5000)

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


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, scaled=scaled5000)

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


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, scaled=scaled5000)
    b = MinHash(0, 10, scaled=scaled5000)

    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


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, scaled=scaled5000)
    b = MinHash(0, 10, scaled=scaled5000)

    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)


def test_distance_matrix(track_abundance):
    import numpy

    siglist = [next(signature.load_signatures(utils.get_test_data(f)))
               for f in utils.SIG_FILES]

    D1 = numpy.zeros([len(siglist), len(siglist)])
    D2 = numpy.zeros([len(siglist), len(siglist)])

    for i, E in enumerate(siglist):
        for j, E2 in enumerate(siglist):
            if i < j:
                continue
            similarity = E.similarity(E2, track_abundance)
            D2[i][j] = similarity
            D2[j][i] = similarity

    for i, E in enumerate(siglist):
        for j, E2 in enumerate(siglist):
            D1[i][j] = E.similarity(E2, track_abundance)

    assert numpy.array_equal(D1, D2)


def test_remove_many(track_abundance):
    a = MinHash(0, 10, track_abundance=track_abundance, scaled=scaled5000)

    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.hashes)


def test_add_many(track_abundance):
    a = MinHash(0, 10, track_abundance=track_abundance, scaled=scaled5000)
    b = MinHash(0, 10, track_abundance=track_abundance, scaled=scaled5000)

    a.add_many(list(range(0, 100, 2)))
    a.add_many(list(range(0, 100, 2)))    # => abundance = 2

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

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

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


def test_set_abundances_huge():
    max_hash = 4000000
    a = MinHash(0, 10, track_abundance=True,
                scaled=_get_scaled_for_max_hash(max_hash))

    hashes = list(range(max_hash))
    abundances = itertools.repeat(2)

    a.set_abundances(dict(zip(hashes, abundances)))


def test_try_change_hashes(track_abundance):
    a = MinHash(0, 10, track_abundance=track_abundance, scaled=scaled5000)
    b = MinHash(0, 10, track_abundance=track_abundance, scaled=scaled5000)

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

    h = a.hashes
    with pytest.raises(RuntimeError):
        h[5] = 10


def test_flatten():
    # test behavior with scaled
    scaled = _get_scaled_for_max_hash(35)
    mh = MinHash(0, 4, track_abundance=True, scaled=scaled)
    assert mh.max_hash == 35

    mh.add_hash(10)
    mh.add_hash(10)
    mh.add_hash(10)
    mh.add_hash(20)
    mh.add_hash(20)
    mh.add_hash(30)
    mh.add_hash(30)
    mh.add_hash(30)

    assert mh.hashes[10] == 3
    assert mh.hashes[20] == 2
    assert mh.hashes[30] == 3

    mh2 = mh.flatten()

    assert mh2.hashes[10] == 1
    assert mh2.hashes[20] == 1
    assert mh2.hashes[30] == 1
    assert len(mh2) == 3


def test_add_kmer(track_abundance):
    # test add_kmer method
    mh1 = MinHash(0, 4, scaled=1, track_abundance=track_abundance)
    mh2 = MinHash(0, 4, scaled=1, track_abundance=track_abundance)

    mh1.add_sequence('ATGCGTGC')
    a = mh1.hashes

    mh2.add_kmer('ATGC')
    mh2.add_kmer('TGCG')
    mh2.add_kmer('GCGT')
    mh2.add_kmer('CGTG')
    mh2.add_kmer('GTGC')
    b = mh2.hashes

    assert set(a.items()) == set(b.items())


def test_add_kmer_too_long(track_abundance):
    # test add_kmer method - should only take length k
    mh1 = MinHash(0, 4, scaled=1, track_abundance=track_abundance)

    with pytest.raises(ValueError):
        mh1.add_kmer('ATGCGTGC')


def test_get_mins_deprecated(track_abundance):
    mh = MinHash(0, 21, scaled=1, track_abundance=track_abundance)
    mins = (28945103950853965, 74690756200987412, 82962372765557409)

    mh.add_many(mins)
    mh.add_many(mins)
    mh.add_many(mins)
    mh.add_many(mins)

    with pytest.warns(DeprecationWarning):
        assert set(mh.get_mins()) == set(mins)
        if track_abundance:
            d = mh.get_mins(with_abundance=True)
            for k in mins:
                assert d[k] == 4
            assert len(d) == len(mins)


def test_get_hashes_deprecated(track_abundance):
    mh = MinHash(0, 21, scaled=1, track_abundance=track_abundance)
    mins = (28945103950853965, 74690756200987412, 82962372765557409)

    mh.add_many(mins)
    mh.add_many(mins)
    mh.add_many(mins)
    mh.add_many(mins)

    with pytest.warns(DeprecationWarning):
        assert set(mh.get_hashes()) == set(mins)


def test_downsample_num(track_abundance):
    # test downsample(num=...) function
    mh = MinHash(10, 21, track_abundance=track_abundance)
    for i in range(20):
        mh.add_hash(i)

    assert mh.num == 10
    assert len(mh) == 10

    assert list(sorted(mh.hashes)) == list(range(10))

    mh2 = mh.downsample(num=5)
    assert mh2.num == 5
    assert len(mh2) == 5

    assert list(sorted(mh2.hashes)) == list(range(5))


def test_downsample_scaled(track_abundance):
    # test downsample(scaled...) method
    mh = MinHash(0, 21, scaled=1, track_abundance=track_abundance)

    mins = (1, 2, 3,
            9223372036854775808 + 1, 9223372036854775808 + 2,
            9223372036854775808 + 3)
    mh.add_many(mins)

    assert len(mh) == 6
    assert list(sorted(mh.hashes)) == list(mins)

    mh2 = mh.downsample(scaled=2)
    print(mh.max_hash, mh2.max_hash)

    assert len(mh2) == 3
    assert list(sorted(mh2.hashes)) == list(mins[:3])


def test_is_molecule_type_1(track_abundance):
    mh = MinHash(1, 21, track_abundance=track_abundance)
    assert mh.moltype == 'DNA'
    assert mh.is_dna
    assert not mh.is_protein
    assert not mh.hp
    assert not mh.dayhoff


def test_is_molecule_type_2(track_abundance):
    mh = MinHash(1, 21, track_abundance=track_abundance, is_protein=True)
    assert mh.moltype == 'protein'
    assert not mh.is_dna
    assert mh.is_protein
    assert not mh.hp
    assert not mh.dayhoff


def test_is_molecule_type_3(track_abundance):
    mh = MinHash(1, 21, track_abundance=track_abundance, hp=True)
    assert mh.moltype == 'hp'
    assert not mh.is_dna
    assert not mh.is_protein
    assert mh.hp
    assert not mh.dayhoff



def test_is_molecule_type_4(track_abundance):
    mh = MinHash(1, 21, track_abundance=track_abundance, dayhoff=True)
    assert mh.moltype == 'dayhoff'
    assert not mh.is_dna
    assert not mh.is_protein
    assert not mh.hp
    assert mh.dayhoff