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test_signature.py
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test_signature.py
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import os
import pytest
import sourmash
from sourmash.signature import SourmashSignature, save_signatures, \
load_signatures, load_one_signature, FrozenSourmashSignature
import sourmash_tst_utils as utils
from sourmash.minhash import MinHash, FrozenMinHash
from sourmash_tst_utils import SourmashCommandFailed
def test_minhash_copy(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig = SourmashSignature(e, name='foo')
f = e.copy()
assert e == f
def test_sig_copy(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig1 = SourmashSignature(e, name='foo')
sig2 = sig1.copy()
assert sig1 == sig2
def test_sig_copy_frozen(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig1 = SourmashSignature(e, name='foo')
sig2 = sig1.copy()
assert sig1 == sig2
with pytest.raises(TypeError) as e:
sig2.minhash.add_hash(5)
assert 'FrozenMinHash does not support modification' in str(e.value)
def test_sig_copy_frozen_mutable(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig1 = SourmashSignature(e, name='foo')
sig1.minhash = sig1.minhash.to_mutable()
sig2 = sig1.copy()
assert sig1 == sig2
with pytest.raises(TypeError) as e:
sig2.minhash.add_hash(5)
assert 'FrozenMinHash does not support modification' in str(e.value)
def test_compare(track_abundance):
# same content, same name -> equal
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig1 = SourmashSignature(e, name='foo')
f = MinHash(n=1, ksize=20, track_abundance=track_abundance)
f.add_kmer("AT" * 10)
sig2 = SourmashSignature(f, name='foo')
assert e == f
def test_compare_ne(track_abundance):
# same content, different names -> different
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig1 = SourmashSignature(e, name='foo')
f = MinHash(n=1, ksize=20, track_abundance=track_abundance)
f.add_kmer("AT" * 10)
sig2 = SourmashSignature(f, name='bar')
assert sig1 != sig2
def test_compare_ne2(track_abundance):
# same content, different filename -> different
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig1 = SourmashSignature(e, name='foo', filename='a')
f = MinHash(n=1, ksize=20, track_abundance=track_abundance)
f.add_kmer("AT" * 10)
sig2 = SourmashSignature(f, name='foo', filename='b')
assert sig1 != sig2
assert sig2 != sig1
def test_compare_ne2_reverse(track_abundance):
# same content, one has filename, other does not -> different
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig1 = SourmashSignature(e, name='foo')
f = MinHash(n=1, ksize=20, track_abundance=track_abundance)
f.add_kmer("AT" * 10)
sig2 = SourmashSignature(f, filename='b')
assert sig2 != sig1
assert sig1 != sig2
def test_hashable(track_abundance):
# check: can we use signatures as keys in dictionaries and sets?
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig = SourmashSignature(e)
x = set()
x.add(sig)
def test_str(track_abundance):
# signatures should be printable
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig = SourmashSignature(e)
print(sig)
assert repr(sig) == "SourmashSignature('', 59502a74)"
sig._name = 'fizbar'
assert repr(sig) == 'SourmashSignature(\'fizbar\', 59502a74)'
def test_roundtrip(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig = SourmashSignature(e)
s = save_signatures([sig])
siglist = list(load_signatures(s))
sig2 = siglist[0]
e2 = sig2.minhash
assert sig.similarity(sig2) == 1.0
assert sig2.similarity(sig) == 1.0
assert isinstance(sig, SourmashSignature)
assert not isinstance(sig, FrozenSourmashSignature)
assert isinstance(sig2, FrozenSourmashSignature)
assert isinstance(e, MinHash)
assert isinstance(sig.minhash, FrozenMinHash)
assert isinstance(sig2.minhash, FrozenMinHash)
def test_roundtrip_mutable_frozen(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig = SourmashSignature(e)
assert isinstance(sig.minhash, FrozenMinHash)
sig.minhash = sig.minhash.to_mutable()
sig2 = sig.to_frozen()
assert isinstance(sig2.minhash, FrozenMinHash)
def test_load_signature_ksize_nonint(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
sig = SourmashSignature(e)
s = save_signatures([sig])
siglist = list(load_signatures(s, ksize='20'))
sig2 = siglist[0]
e2 = sig2.minhash
assert sig.similarity(sig2) == 1.0
assert sig2.similarity(sig) == 1.0
def test_roundtrip_empty(track_abundance):
# edge case, but: empty minhash? :)
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig = SourmashSignature(e)
s = save_signatures([sig])
siglist = list(load_signatures(s))
sig2 = siglist[0]
e2 = sig2.minhash
assert sig.similarity(sig2) == 0
assert sig2.similarity(sig) == 0
def test_roundtrip_scaled(track_abundance):
e = MinHash(n=0, ksize=20, track_abundance=track_abundance,
max_hash=10)
e.add_hash(5)
sig = SourmashSignature(e)
s = save_signatures([sig])
siglist = list(load_signatures(s))
sig2 = siglist[0]
e2 = sig2.minhash
assert e.scaled == e2.scaled
assert sig.similarity(sig2) == 1.0
assert sig2.similarity(sig) == 1.0
def test_roundtrip_seed(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance,
seed=10)
e.add_hash(5)
sig = SourmashSignature(e)
s = save_signatures([sig])
siglist = list(load_signatures(s))
sig2 = siglist[0]
e2 = sig2.minhash
assert e.seed == e2.seed
assert sig.similarity(sig2) == 1.0
assert sig2.similarity(sig) == 1.0
def test_similarity_downsample(track_abundance):
e = MinHash(n=0, ksize=20, track_abundance=track_abundance,
max_hash=2**63)
f = MinHash(n=0, ksize=20, track_abundance=track_abundance,
max_hash=2**2)
e.add_hash(1)
e.add_hash(5)
assert len(e.hashes) == 2
f.add_hash(1)
f.add_hash(5) # should be discarded due to max_hash
assert len(f.hashes) == 1
ee = SourmashSignature(e)
ff = SourmashSignature(f)
with pytest.raises(ValueError) as e: # mismatch in max_hash
ee.similarity(ff)
assert 'mismatch in scaled; comparison fail' in str(e.value)
x = ee.similarity(ff, downsample=True)
assert round(x, 1) == 1.0
def test_add_sequence_bad_dna(track_abundance):
# test add_sequence behavior on bad DNA
mh = MinHash(n=1, ksize=21)
sig = SourmashSignature(mh)
with pytest.raises(ValueError) as e:
sig.add_sequence("N" * 21, force=False)
assert 'invalid DNA character in input k-mer: NNNNNNNNNNNNNNNNNNNNN' in str(e.value)
def test_md5(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_hash(5)
sig = SourmashSignature(e)
assert sig.md5sum() == 'eae27d77ca20db309e056e3d2dcd7d69', sig.md5sum()
def test_str_1(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig = SourmashSignature(e, name='foo')
assert str(sig) == 'foo'
def test_str_2(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig = SourmashSignature(e, filename='foo.txt')
assert str(sig) == 'foo.txt'
def test_str_3(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig = SourmashSignature(e, name='foo',
filename='foo.txt')
assert str(sig) == 'foo'
def test_name_4(track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig = SourmashSignature(e)
assert str(sig) == sig.md5sum()[:8]
def test_save_load_multisig(track_abundance):
e1 = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig1 = SourmashSignature(e1)
e2 = MinHash(n=1, ksize=25, track_abundance=track_abundance)
sig2 = SourmashSignature(e2)
x = save_signatures([sig1, sig2])
y = list(load_signatures(x))
print(x)
assert len(y) == 2
assert sig1 in y # order not guaranteed, note.
assert sig2 in y
assert sig1 != sig2
def test_load_one_fail_nosig(track_abundance):
x = save_signatures([])
print((x,))
with pytest.raises(ValueError):
y = load_one_signature(x)
def test_load_one_succeed(track_abundance):
e1 = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig1 = SourmashSignature(e1)
x = save_signatures([sig1])
y = load_one_signature(x)
assert sig1 == y
def test_load_one_fail_multisig(track_abundance):
e1 = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig1 = SourmashSignature(e1)
e2 = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig2 = SourmashSignature(e2)
x = save_signatures([sig1, sig2])
with pytest.raises(ValueError):
y = load_one_signature(x)
def test_save_minified(track_abundance):
e1 = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig1 = SourmashSignature(e1, name="foo")
e2 = MinHash(n=1, ksize=25, track_abundance=track_abundance)
sig2 = SourmashSignature(e2, name="bar baz")
x = save_signatures([sig1, sig2])
assert b'\n' not in x
assert len(x.split(b'\n')) == 1
y = list(load_signatures(x))
assert len(y) == 2
assert any(sig.name == 'foo' for sig in y)
assert any(sig.name == 'bar baz' for sig in y)
def test_load_minified(track_abundance):
sigfile = utils.get_test_data('genome-s10+s11.sig')
sigs = load_signatures(sigfile)
minified = save_signatures(sigs)
with open(sigfile, 'r') as f:
orig_file = f.read()
assert len(minified) < len(orig_file)
assert b'\n' not in minified
def test_load_compressed(track_abundance):
e1 = MinHash(n=1, ksize=20, track_abundance=track_abundance)
sig1 = SourmashSignature(e1)
x = save_signatures([sig1], compression=5)
y = load_one_signature(x)
assert sig1 == y
sigfile = utils.get_test_data('genome-s10+s11.sig.gz')
sigs = load_signatures(sigfile)
def test_binary_fp(tmpdir, track_abundance):
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
path = tmpdir.join("1.sig")
with open(str(path), 'wb') as fp:
sig = SourmashSignature(e)
s = save_signatures([sig], fp)
def test_load_signatures_no_file_do_raise(tmpdir):
path = tmpdir.join("dne.sig")
siglist = load_signatures(path, do_raise=True)
with pytest.raises(Exception):
list(siglist)
def test_load_signatures_no_file_do_not_raise(tmpdir):
path = tmpdir.join("dne.sig")
siglist = load_signatures(path)
siglist = list(siglist)
assert not siglist
def test_max_containment():
mh1 = MinHash(0, 21, scaled=1, track_abundance=False)
mh2 = MinHash(0, 21, scaled=1, track_abundance=False)
mh1.add_many((1, 2, 3, 4))
mh2.add_many((1, 5))
ss1 = SourmashSignature(mh1)
ss2 = SourmashSignature(mh2)
assert ss1.contained_by(ss2) == 1/4
assert ss2.contained_by(ss1) == 1/2
assert ss1.max_containment(ss2) == 1/2
assert ss2.max_containment(ss1) == 1/2
def test_max_containment_empty():
mh1 = MinHash(0, 21, scaled=1, track_abundance=False)
mh2 = MinHash(0, 21, scaled=1, track_abundance=False)
mh1.add_many((1, 2, 3, 4))
ss1 = SourmashSignature(mh1)
ss2 = SourmashSignature(mh2)
assert ss1.contained_by(ss2) == 0
assert ss2.contained_by(ss1) == 0
assert ss1.max_containment(ss2) == 0
assert ss2.max_containment(ss1) == 0
def test_max_containment_equal():
mh1 = MinHash(0, 21, scaled=1, track_abundance=False)
mh2 = MinHash(0, 21, scaled=1, track_abundance=False)
mh1.add_many((1, 2, 3, 4))
mh2.add_many((1, 2, 3, 4))
ss1 = SourmashSignature(mh1)
ss2 = SourmashSignature(mh2)
assert ss1.contained_by(ss2) == 1
assert ss2.contained_by(ss1) == 1
assert ss1.max_containment(ss2) == 1
assert ss2.max_containment(ss1) == 1
def test_containment_ANI():
f1 = utils.get_test_data('2.fa.sig')
f2 = utils.get_test_data('2+63.fa.sig')
ss1 = sourmash.load_one_signature(f1, ksize=31)
ss2 = sourmash.load_one_signature(f2, ksize=31)
s1_cont_s2 = ss1.containment_ani(ss2, estimate_ci =True)
s2_cont_s1 = ss2.containment_ani(ss1, estimate_ci =True)
print("\nss1 contained by ss2", s1_cont_s2)
print("ss2 contained by ss1", s2_cont_s1)
assert (round(s1_cont_s2.ani,3), s1_cont_s2.ani_low, s1_cont_s2.ani_high) == (1.0,1.0,1.0)
assert (round(s2_cont_s1.ani,3), round(s2_cont_s1.ani_low,3), round(s2_cont_s1.ani_high,3)) == (0.966, 0.965, 0.967)
s1_mc_s2 = ss1.max_containment_ani(ss2, estimate_ci =True)
s2_mc_s1 = ss2.max_containment_ani(ss1, estimate_ci =True)
print("mh1 max containment", s1_mc_s2)
print("mh2 max containment", s2_mc_s1)
s1_mc_s2.size_is_inaccurate = False
s2_mc_s1.size_is_inaccurate = False
assert s1_mc_s2 == s2_mc_s1
assert (round(s1_mc_s2.ani, 3), round(s1_mc_s2.ani_low, 3), round(s1_mc_s2.ani_high, 3)) == (1.0,1.0,1.0)
def test_containment_ANI_precalc_containment():
f1 = utils.get_test_data('47+63.fa.sig')
f2 = utils.get_test_data('2+63.fa.sig')
ss1 = sourmash.load_one_signature(f1, ksize=31)
ss2 = sourmash.load_one_signature(f2, ksize=31)
# precalc containments and assert same results
s1c = ss1.contained_by(ss2)
s2c = ss2.contained_by(ss1)
mc = max(s1c, s2c)
assert ss1.containment_ani(ss2, estimate_ci=True) == ss1.containment_ani(ss2, containment=s1c, estimate_ci=True)
assert ss2.containment_ani(ss1) == ss2.containment_ani(ss1, containment=s2c)
assert ss1.max_containment_ani(ss2) == ss2.max_containment_ani(ss1)
assert ss1.max_containment_ani(ss2) == ss1.max_containment_ani(ss2, max_containment=mc)
assert ss1.max_containment_ani(ss2) == ss2.max_containment_ani(ss1, max_containment=mc)
def test_avg_containment():
f1 = utils.get_test_data('47+63.fa.sig')
f2 = utils.get_test_data('2+63.fa.sig')
ss1 = sourmash.load_one_signature(f1, ksize=31)
ss2 = sourmash.load_one_signature(f2, ksize=31)
# check average_containment_ani
ac_s1 = ss1.avg_containment(ss2)
ac_s2 = ss2.avg_containment(ss1)
assert ac_s1 == ac_s2 == (ss1.contained_by(ss2) + ss2.contained_by(ss1))/2 == 0.6619979467456603
def test_avg_containment_ani():
f1 = utils.get_test_data('47+63.fa.sig')
f2 = utils.get_test_data('2+63.fa.sig')
ss1 = sourmash.load_one_signature(f1, ksize=31)
ss2 = sourmash.load_one_signature(f2, ksize=31)
# check average_containment_ani
ac_s1 = ss1.avg_containment_ani(ss2)
ac_s2 = ss2.avg_containment_ani(ss1)
assert ac_s1 == ac_s2 == (ss1.containment_ani(ss2).ani + ss2.containment_ani(ss1).ani)/2
def test_containment_ANI_downsample():
f2 = utils.get_test_data('2+63.fa.sig')
f3 = utils.get_test_data('47+63.fa.sig')
ss2 = sourmash.load_one_signature(f2, ksize=31)
ss3 = sourmash.load_one_signature(f3, ksize=31)
# check that downsampling works properly
print(ss2.minhash.scaled)
ss2 = ss2.to_mutable()
ss2.minhash = ss2.minhash.downsample(scaled=2000)
assert ss2.minhash.scaled != ss3.minhash.scaled
ds_s3c = ss2.containment_ani(ss3, downsample=True)
ds_s4c = ss3.containment_ani(ss2, downsample=True)
mc_w_ds_1 = ss2.max_containment_ani(ss3, downsample=True)
mc_w_ds_2 = ss3.max_containment_ani(ss2, downsample=True)
with pytest.raises(ValueError) as e:
ss2.containment_ani(ss3)
assert "ValueError: mismatch in scaled; comparison fail" in e
with pytest.raises(ValueError) as e:
ss2.max_containment_ani(ss3)
assert "ValueError: mismatch in scaled; comparison fail" in e
ss3 = ss3.to_mutable()
ss3.minhash = ss3.minhash.downsample(scaled=2000)
assert ss2.minhash.scaled == ss3.minhash.scaled
ds_s3c_manual = ss2.containment_ani(ss3)
ds_s4c_manual = ss3.containment_ani(ss2)
ds_mc_manual = ss2.max_containment_ani(ss3)
assert ds_s3c == ds_s3c_manual
assert ds_s4c == ds_s4c_manual
assert mc_w_ds_1 == mc_w_ds_2 == ds_mc_manual
def test_jaccard_ANI():
f1 = utils.get_test_data('2.fa.sig')
f2 = utils.get_test_data('2+63.fa.sig')
ss1 = sourmash.load_one_signature(f1, ksize=31)
ss2 = sourmash.load_one_signature(f2)
print("\nJACCARD_ANI", ss1.jaccard_ani(ss2))
s1_jani_s2 = ss1.jaccard_ani(ss2)
s2_jani_s1 = ss2.jaccard_ani(ss1)
assert s1_jani_s2 == s2_jani_s1
assert (s1_jani_s2.ani, s1_jani_s2.p_nothing_in_common, s1_jani_s2.jaccard_error) == (0.9783711630110239, 0.0, 3.891666770716877e-07)
def test_jaccard_ANI_untrustworthy():
f1 = utils.get_test_data('2.fa.sig')
f2 = utils.get_test_data('2+63.fa.sig')
ss1 = sourmash.load_one_signature(f1, ksize=31)
ss2 = sourmash.load_one_signature(f2)
print("\nJACCARD_ANI", ss1.jaccard_ani(ss2))
s1_jani_s2 = ss1.jaccard_ani(ss2, err_threshold=1e-7)
# since size is inaccurate on 2.fa.sig, need to override to be able to get ani
s1_jani_s2.size_is_inaccurate = False
assert s1_jani_s2.ani == None
assert s1_jani_s2.je_exceeds_threshold==True
assert s1_jani_s2.je_threshold == 1e-7
def test_jaccard_ANI_precalc_jaccard():
f1 = utils.get_test_data('47+63.fa.sig')
f2 = utils.get_test_data('2+63.fa.sig')
ss1 = sourmash.load_one_signature(f1, ksize=31)
ss2 = sourmash.load_one_signature(f2)
# precalc jaccard and assert same result
jaccard = ss1.jaccard(ss2)
print("\nJACCARD_ANI", ss1.jaccard_ani(ss2,jaccard=jaccard))
assert ss1.jaccard_ani(ss2) == ss1.jaccard_ani(ss2, jaccard=jaccard) == ss2.jaccard_ani(ss1, jaccard=jaccard)
wrong_jaccard = jaccard - 0.1
assert ss1.jaccard_ani(ss2) != ss1.jaccard_ani(ss2, jaccard=wrong_jaccard)
def test_jaccard_ANI_downsample():
f1 = utils.get_test_data('47+63.fa.sig')
f2 = utils.get_test_data('2+63.fa.sig')
ss1 = sourmash.load_one_signature(f1, ksize=31)
ss2 = sourmash.load_one_signature(f2)
print(ss1.minhash.scaled)
ss1 = ss1.to_mutable()
ss1.minhash = ss1.minhash.downsample(scaled=2000)
assert ss1.minhash.scaled != ss2.minhash.scaled
with pytest.raises(ValueError) as e:
ss1.jaccard_ani(ss2)
assert "ValueError: mismatch in scaled; comparison fail" in e
ds_s1c = ss1.jaccard_ani(ss2, downsample=True)
ds_s2c = ss2.jaccard_ani(ss1, downsample=True)
ss2 = ss2.to_mutable()
ss2.minhash = ss2.minhash.downsample(scaled=2000)
assert ss1.minhash.scaled == ss2.minhash.scaled
ds_j_manual = ss1.jaccard_ani(ss2)
assert ds_s1c == ds_s2c == ds_j_manual
def test_frozen_signature_update_1(track_abundance):
# setting .name should fail on a FrozenSourmashSignature
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
ss = SourmashSignature(e, name='foo').to_frozen()
with pytest.raises(ValueError):
ss.name = 'foo2'
def test_frozen_signature_update_2(track_abundance):
# setting .minhash should fail on a FrozenSourmashSignature
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
e2 = e.copy_and_clear()
ss = SourmashSignature(e, name='foo').to_frozen()
with pytest.raises(ValueError):
ss.minhash = e2
def test_frozen_signature_update_3(track_abundance):
# setting .minhash should succeed with update() context manager
e = MinHash(n=1, ksize=20, track_abundance=track_abundance)
e.add_kmer("AT" * 10)
ss = SourmashSignature(e, name='foo').to_frozen()
with ss.update() as ss2:
ss2.name = 'foo2'
assert ss2.name == 'foo2'