def test_sbt_gather_threshold_1():
# test gather() method, in some detail
factory = GraphFactory(31, 1e5, 4)
tree = SBT(factory, d=2)
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)
tree.insert(sig47)
tree.insert(sig63)
tree.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 tree.gather(SourmashSignature(new_mh))
# add one hash
new_mh.add_hash(mins.pop())
assert len(new_mh) == 1
results = tree.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 = tree.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 = tree.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.
print('len mh', len(new_mh))
results = tree.gather(SourmashSignature(new_mh), threshold_bp=5000)
assert not results
def test_sbt_gather_threshold_5():
# test gather() method above threshold
factory = GraphFactory(31, 1e5, 4)
tree = SBT(factory, d=2)
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)
tree.insert(sig47)
tree.insert(sig63)
tree.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 = tree.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
# now, check with a threshold_bp that should be meet-able.
results = tree.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 is None
def test_gather_multiple_return(c):
# test gather() method number of returns
sig2file = utils.get_test_data('2.fa.sig')
sig47file = utils.get_test_data('47.fa.sig')
sig63file = utils.get_test_data('63.fa.sig')
sig2 = load_one_signature(sig2file, ksize=31)
sig47 = load_one_signature(sig47file, ksize=31)
sig63 = load_one_signature(sig63file, ksize=31)
# construct LCA Database
factory = GraphFactory(31, 1e5, 4)
tree = SBT(factory, d=2)
tree.insert(sig2)
tree.insert(sig47)
tree.insert(sig63)
# now, run gather. how many results do we get, and are they in the
# right order?
results = tree.gather(sig63)
print(len(results))
assert len(results) == 2
assert results[0][0] == 1.0
