def test_get_centroids(self):
ramifier = RotatingRamifier.from_file(4, KMER_ROTATION)
db = GridCoverDB(sqlite3.connect(':memory:'),
ramifier=ramifier,
box_side_len=0.5)
db.py_add_point_to_cluster(np.array([0., 0., 0., 0.]), KMER_30 + 'A')
db.py_add_point_to_cluster(np.array([0., 0., 0., 0.]), KMER_30 + 'T')
db.py_add_point_to_cluster(np.array([1., 0., 0., 0.]), KMER_30 + 'C')
db.commit()
centroids = db.centroids()
self.assertEqual(centroids.shape, (2, 4))
def test_add_kmer(self):
ramifier = RotatingRamifier.from_file(4, KMER_ROTATION)
db = GridCoverDB(sqlite3.connect(':memory:'),
ramifier=ramifier,
box_side_len=0.5)
db.py_add_point_to_cluster(np.array([0., 0., 0., 0.]), KMER_31)
db.commit()
members = db.py_get_cluster_members(0)
self.assertEqual(len(members), 1)
self.assertIn(KMER_31,
[reverse_convert_kmer(member) for member in members])
def test_pre_build_blooms(self):
ramifier = RotatingRamifier.from_file(4, KMER_ROTATION)
db = GridCoverDB(sqlite3.connect(':memory:'),
ramifier=ramifier,
box_side_len=0.5)
db.py_add_point_to_cluster(np.array([0., 0., 0., 0.]), KMER_30 + 'A')
db.py_add_point_to_cluster(np.array([0., 0., 0., 0.]), KMER_30 + 'T')
db.py_add_point_to_cluster(np.array([1., 0., 0., 0.]), KMER_30 + 'C')
db.commit()
for centroid_id in [0, 1]:
db.build_and_store_bloom_grid(centroid_id)
bg_0 = db.retrieve_bloom_grid(0)
bg_1 = db.retrieve_bloom_grid(1)
self.assertEqual(max(bg_0.py_count_grid_contains(KMER_30 + 'A')),
32 - bg_0.col_k)
self.assertEqual(max(bg_1.py_count_grid_contains(KMER_30 + 'C')),
32 - bg_1.col_k)
self.assertRaises(IndexError, lambda: db.retrieve_bloom_grid(2))
def test_merge_dbs(self):
ramifier = RotatingRamifier.from_file(4, KMER_ROTATION)
db1 = GridCoverDB(sqlite3.connect(':memory:'),
ramifier=ramifier,
box_side_len=0.5)
db1.py_add_point_to_cluster(np.array([0., 0., 0., 0.]), KMER_30 + 'A')
db1.py_add_point_to_cluster(np.array([1., 0., 0., 0.]), KMER_30 + 'T')
db1.commit()
db2 = GridCoverDB(sqlite3.connect(':memory:'),
ramifier=ramifier,
box_side_len=0.5)
db2.py_add_point_to_cluster(np.array([0., 0., 0., 0.]), KMER_30 + 'C')
db2.py_add_point_to_cluster(np.array([1., 1., 0., 0.]), KMER_30 + 'G')
db2.commit()
db1.load_other(db2)
centroids = db1.centroids()
self.assertEqual(centroids.shape, (3, 4))
kmers = [el[1] for el in db1.get_kmers()]
self.assertEqual(len(kmers), 4)
for char in 'ATCG':
self.assertIn(KMER_30 + char, kmers)