def test_linear_index_moltype_select():
# this loads two ksizes(21, 30), and two moltypes (DNA and protein)
filename = utils.get_test_data('genome-s10+s11.sig')
siglist = sourmash.load_signatures(filename)
linear = LinearIndex()
for ss in siglist:
linear.insert(ss)
# select most specific DNA
linear2 = linear.select(ksize=30, moltype='DNA')
assert len(linear2) == 1
# select most specific protein
linear2 = linear.select(ksize=30, moltype='protein')
assert len(linear2) == 1
# can leave off ksize, selects all ksizes
linear2 = linear.select(moltype='DNA')
assert len(linear2) == 2
# can leave off ksize, selects all ksizes
linear2 = linear.select(moltype='protein')
assert len(linear2) == 2
# select something impossible
linear2 = linear.select(ksize=4)
assert len(linear2) == 0
def test_linear_index_save():
sig2 = utils.get_test_data('2.fa.sig')
sig47 = utils.get_test_data('47.fa.sig')
sig63 = utils.get_test_data('63.fa.sig')
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss47 = sourmash.load_one_signature(sig47)
ss63 = sourmash.load_one_signature(sig63)
linear = LinearIndex()
linear.insert(ss2)
linear.insert(ss47)
linear.insert(ss63)
with utils.TempDirectory() as location:
filename = os.path.join(location, 'foo')
linear.save(filename)
from sourmash import load_signatures
si = set(load_signatures(filename))
x = {ss2, ss47, ss63}
print(len(si))
print(len(x))
print(si)
print(x)
assert si == x, si
def test_linear_index_gather():
sig2 = utils.get_test_data('2.fa.sig')
sig47 = utils.get_test_data('47.fa.sig')
sig63 = utils.get_test_data('63.fa.sig')
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss47 = sourmash.load_one_signature(sig47)
ss63 = sourmash.load_one_signature(sig63)
lidx = LinearIndex()
lidx.insert(ss2)
lidx.insert(ss47)
lidx.insert(ss63)
matches = lidx.gather(ss2)
assert len(matches) == 1
assert matches[0][0] == 1.0
assert matches[0][1] == ss2
matches = lidx.gather(ss47)
assert len(matches) == 2
assert matches[0][0] == 1.0
assert matches[0][1] == ss47
assert round(matches[1][0], 2) == 0.49
assert matches[1][1] == ss63
def test_simple_index(n_children):
factory = GraphFactory(5, 100, 3)
root = SBT(factory, d=n_children)
leaf1 = Leaf("a", factory())
leaf1.data.count("AAAAA")
leaf1.data.count("AAAAT")
leaf1.data.count("AAAAC")
leaf2 = Leaf("b", factory())
leaf2.data.count("AAAAA")
leaf2.data.count("AAAAT")
leaf2.data.count("AAAAG")
leaf3 = Leaf("c", factory())
leaf3.data.count("AAAAA")
leaf3.data.count("AAAAT")
leaf3.data.count("CAAAA")
leaf4 = Leaf("d", factory())
leaf4.data.count("AAAAA")
leaf4.data.count("CAAAA")
leaf4.data.count("GAAAA")
leaf5 = Leaf("e", factory())
leaf5.data.count("AAAAA")
leaf5.data.count("AAAAT")
leaf5.data.count("GAAAA")
root.add_node(leaf1)
root.add_node(leaf2)
root.add_node(leaf3)
root.add_node(leaf4)
root.add_node(leaf5)
def search_kmer(obj, seq):
return obj.data.get(seq)
kmers = ["AAAAA", "AAAAT", "AAAAG", "CAAAA", "GAAAA"]
linear = LinearIndex()
linear.insert(leaf1)
linear.insert(leaf2)
linear.insert(leaf3)
linear.insert(leaf4)
linear.insert(leaf5)
for kmer in kmers:
assert set(root.find(search_kmer,
kmer)) == set(linear.find(search_kmer, kmer))
print("-----")
print([x.metadata for x in root.find(search_kmer, "AAAAA")])
print([x.metadata for x in root.find(search_kmer, "AAAAT")])
print([x.metadata for x in root.find(search_kmer, "AAAAG")])
print([x.metadata for x in root.find(search_kmer, "CAAAA")])
print([x.metadata for x in root.find(search_kmer, "GAAAA")])
def test_linear_gather_threshold_1():
# test gather() method, in some detail
sig2 = load_one_signature(utils.get_test_data('2.fa.sig'), ksize=31)
sig47 = load_one_signature(utils.get_test_data('47.fa.sig'), ksize=31)
sig63 = load_one_signature(utils.get_test_data('63.fa.sig'), ksize=31)
linear = LinearIndex()
linear.insert(sig47)
linear.insert(sig63)
linear.insert(sig2)
# now construct query signatures with specific numbers of hashes --
# note, these signatures all have scaled=1000.
mins = list(sorted(sig2.minhash.get_mins()))
new_mh = sig2.minhash.copy_and_clear()
# query with empty hashes
assert not new_mh
assert not linear.gather(SourmashSignature(new_mh))
# add one hash
new_mh.add_hash(mins.pop())
assert len(new_mh) == 1
results = linear.gather(SourmashSignature(new_mh))
assert len(results) == 1
containment, match_sig, name = results[0]
assert containment == 1.0
assert match_sig == sig2
assert name is None
# check with a threshold -> should be no results.
results = linear.gather(SourmashSignature(new_mh), threshold_bp=5000)
assert not results
# add three more hashes => length of 4
new_mh.add_hash(mins.pop())
new_mh.add_hash(mins.pop())
new_mh.add_hash(mins.pop())
assert len(new_mh) == 4
results = linear.gather(SourmashSignature(new_mh))
assert len(results) == 1
containment, match_sig, name = results[0]
assert containment == 1.0
assert match_sig == sig2
assert name is None
# check with a too-high threshold -> should be no results.
results = linear.gather(SourmashSignature(new_mh), threshold_bp=5000)
assert not results
def test_linear_index_multik_select():
# this loads three ksizes, 21/31/51
sig2 = utils.get_test_data('2.fa.sig')
siglist = sourmash.load_signatures(sig2)
linear = LinearIndex()
for ss in siglist:
linear.insert(ss)
# select most specifically
linear2 = linear.select(ksize=31, moltype='DNA')
assert len(linear2) == 1
# all are DNA:
linear2 = linear.select(moltype='DNA')
assert len(linear2) == 3
def test_linear_index_search():
sig2 = utils.get_test_data('2.fa.sig')
sig47 = utils.get_test_data('47.fa.sig')
sig63 = utils.get_test_data('63.fa.sig')
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss47 = sourmash.load_one_signature(sig47)
ss63 = sourmash.load_one_signature(sig63)
lidx = LinearIndex()
lidx.insert(ss2)
lidx.insert(ss47)
lidx.insert(ss63)
# now, search for sig2
sr = lidx.search(ss2, threshold=1.0)
print([s[1].name() for s in sr])
assert len(sr) == 1
assert sr[0][1] == ss2
# search for sig47 with lower threshold; search order not guaranteed.
sr = lidx.search(ss47, threshold=0.1)
print([s[1].name() for s in sr])
assert len(sr) == 2
sr.sort(key=lambda x: -x[0])
assert sr[0][1] == ss47
assert sr[1][1] == ss63
# search for sig63 with lower threshold; search order not guaranteed.
sr = lidx.search(ss63, threshold=0.1)
print([s[1].name() for s in sr])
assert len(sr) == 2
sr.sort(key=lambda x: -x[0])
assert sr[0][1] == ss63
assert sr[1][1] == ss47
# search for sig63 with high threshold => 1 match
sr = lidx.search(ss63, threshold=0.8)
print([s[1].name for s in sr])
assert len(sr) == 1
sr.sort(key=lambda x: -x[0])
assert sr[0][1] == ss63
def test_linear_gather_threshold_5():
# test gather() method above threshold
sig2 = load_one_signature(utils.get_test_data('2.fa.sig'), ksize=31)
sig47 = load_one_signature(utils.get_test_data('47.fa.sig'), ksize=31)
sig63 = load_one_signature(utils.get_test_data('63.fa.sig'), ksize=31)
linear = LinearIndex(filename='foo')
linear.insert(sig47)
linear.insert(sig63)
linear.insert(sig2)
# now construct query signatures with specific numbers of hashes --
# note, these signatures all have scaled=1000.
mins = list(sorted(sig2.minhash.get_mins()))
new_mh = sig2.minhash.copy_and_clear()
# add five hashes
for i in range(5):
new_mh.add_hash(mins.pop())
new_mh.add_hash(mins.pop())
new_mh.add_hash(mins.pop())
new_mh.add_hash(mins.pop())
new_mh.add_hash(mins.pop())
# should get a result with no threshold (any match at all is returned)
results = linear.gather(SourmashSignature(new_mh))
assert len(results) == 1
containment, match_sig, name = results[0]
assert containment == 1.0
assert match_sig == sig2
assert name == 'foo'
# now, check with a threshold_bp that should be meet-able.
results = linear.gather(SourmashSignature(new_mh), threshold_bp=5000)
assert len(results) == 1
containment, match_sig, name = results[0]
assert containment == 1.0
assert match_sig == sig2
assert name == 'foo'
def test_linear_index_save_load():
sig2 = utils.get_test_data('2.fa.sig')
sig47 = utils.get_test_data('47.fa.sig')
sig63 = utils.get_test_data('63.fa.sig')
ss2 = sourmash.load_one_signature(sig2, ksize=31)
ss47 = sourmash.load_one_signature(sig47)
ss63 = sourmash.load_one_signature(sig63)
linear = LinearIndex()
linear.insert(ss2)
linear.insert(ss47)
linear.insert(ss63)
with utils.TempDirectory() as location:
filename = os.path.join(location, 'foo')
linear.save(filename)
linear2 = LinearIndex.load(filename)
# now, search for sig2
sr = linear2.search(ss2, threshold=1.0)
print([s[1].name() for s in sr])
assert len(sr) == 1
assert sr[0][1] == ss2