def setup(self):
self.mh = MinHash(500, 21, track_abundance=False)
self.sequences = load_sequences()
self.populated_mh = MinHash(500, 21, track_abundance=False)
for seq in self.sequences:
self.populated_mh.add_sequence(seq)
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]
class TimeMinAbundanceSuite(TimeMinHashSuite):
def setup(self):
TimeMinHashSuite.setup(self)
self.mh = MinHash(500, 21, track_abundance=True)
self.populated_mh = MinHash(500, 21, track_abundance=True)
for seq in self.sequences:
self.populated_mh.add_sequence(seq)
def time_get_mins_abundance(self):
mh = self.populated_mh
for i in range(500):
mh.get_mins(with_abundance=True)
def time_set_abundances(self):
mh = self.mh
mins = self.populated_mh.get_mins(with_abundance=True)
for i in range(500):
mh.set_abundances(mins)
def time_set_abundances_noclear(self):
mh = self.mh
mins = self.populated_mh.get_mins(with_abundance=True)
for i in range(500):
mh.set_abundances(mins, clear=False)
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 setup(self):
self.mh = MinHash(500, 21, track_abundance=True)
self.protein_mh = MinHash(500,
21,
is_protein=True,
track_abundance=True)
self.sequences = load_sequences()
def setup(self):
TimeMinHashSuite.setup(self)
self.mh = MinHash(500, 21, track_abundance=True)
self.populated_mh = MinHash(500, 21, track_abundance=True)
for seq in self.sequences:
self.populated_mh.add_sequence(seq)
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_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 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 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_set_abundances_huge():
max_hash = 4000000
a = MinHash(0, 10, track_abundance=True, max_hash=max_hash)
hashes = list(range(max_hash))
abundances = itertools.repeat(2)
a.set_abundances(dict(zip(hashes, abundances)))
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_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_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 a.get_mins() == b.get_mins()
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_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_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_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_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_mh_angular_similarity_2():
# check actual angular similarity for a second non-trivial case
a = MinHash(0, 20, max_hash=100, track_abundance=True)
b = MinHash(0, 20, max_hash=100, 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_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_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)
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)
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.get_mins()) == 4
def test_mh_jaccard_similarity():
# check actual Jaccard value for a non-trivial case
a = MinHash(0, 20, max_hash=50, track_abundance=False)
b = MinHash(0, 20, max_hash=50, 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.
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_translate_codon(track_abundance):
# Ensure that translation occurs properly
mh = MinHash(10, 6, is_protein=True)
assert "S" == mh.translate_codon('TCT')
assert "S" == mh.translate_codon('TC')
assert "X" == mh.translate_codon("T")
with pytest.raises(ValueError):
mh.translate_codon("")
mh.translate_codon("TCTA")
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)
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
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_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))
def test_set_abundance_clear_3():
a = MinHash(20, 5, False, track_abundance=True)
a.add_hash(10)
assert a.get_mins(with_abundance=True) == {10: 1}
a.set_abundances({20: 1, 30: 4}, clear=False)
assert a.get_mins(with_abundance=True) == {10: 1, 20: 1, 30: 4}
def test_clear_2():
a = MinHash(20, 5, False, track_abundance=False)
a.add_hash(10)
assert a.get_mins() == [10]
a.clear()
assert a.get_mins() == []
def test_clear():
a = MinHash(20, 5, False, track_abundance=True)
a.add_hash(10)
assert a.get_mins(with_abundance=True) == {10: 1}
a.clear()
assert a.get_mins(with_abundance=True) == {}
def test_scaled_property(track_abundance):
scaled = 10000
a = MinHash(0,
10,
track_abundance=track_abundance,
max_hash=round(2**64 / scaled))
assert a.scaled == scaled
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_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
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
class TimeMinAbundanceSuite(TimeMinHashSuite):
def setup(self):
TimeMinHashSuite.setup(self)
self.mh = MinHash(500, 21, track_abundance=True)
self.populated_mh = MinHash(500, 21, track_abundance=True)
for seq in self.sequences:
self.populated_mh.add_sequence(seq)
def time_get_mins_abundance(self):
mh = self.populated_mh
for i in range(500):
mh.get_mins(with_abundance=True)
def time_set_abundances(self):
mh = self.mh
mins = self.populated_mh.get_mins(with_abundance=True)
for i in range(500):
mh.set_abundances(mins)
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)
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)
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))
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
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
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
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
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.get_mins() == d.get_mins()
assert c.compare(d) == 1.0
assert d.compare(c) == 1.0
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
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())
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
