def test_all_coarse_search_grid_cover_tight(self):
grid = GridCoverSearcher.from_filepath(GRID_COVER)
n_hits, n_kmers = 0, 0
for centroid_id, kmer in grid.db.get_kmers():
n_kmers += 1
results = grid.py_coarse_search(kmer, 0.0001)
if centroid_id in results:
n_hits += 1
self.assertEqual(n_hits, n_kmers)
def test_all_search_grid_cover_broad(self):
grid = GridCoverSearcher.from_filepath(GRID_COVER)
n_hits, n_kmers = 0, 0
for _, kmer in grid.db.get_kmers():
n_kmers += 1
results = grid.py_search(kmer, 10)
if kmer in results:
n_hits += 1
self.assertEqual(n_hits, n_kmers)
def test_one_search_grid_cover_exact(self):
grid = GridCoverSearcher.from_filepath(GRID_COVER)
query = KMER_31
results = grid.py_search(query,
0,
inner_metric='needle',
inner_radius=0)
self.assertIn(query, results)
self.assertEqual(len(results), 1)
def test_double_search_grid_cover_tight(self):
grid = GridCoverSearcher.from_filepath(GRID_COVER)
query = KMER_31
grid.py_search(query, 0.0001)
results = grid.py_search(query,
0.0001,
inner_metric='needle',
inner_radius=0.01)
self.assertIn(query, results)
self.assertEqual(len(results), 1)
def test_all_search_grid_cover_tight(self):
grid = GridCoverSearcher.from_filepath(GRID_COVER)
n_hits, n_kmers = 0, 0
for _, kmer in grid.db.get_kmers():
n_kmers += 1
results = grid.py_search(kmer,
0.0001,
inner_metric='needle',
inner_radius=0.01)
if kmer in results:
n_hits += 1
self.assertEqual(n_hits, n_kmers)
def from_filepath(cls, port, filepath, **kwargs):
grid = GridCoverSearcher.from_filepath(filepath)
return cls(port, grid, **kwargs)
def test_one_search_grid_cover_broad(self):
grid = GridCoverSearcher.from_filepath(GRID_COVER)
query = KMER_31
results = grid.py_search(query, 10)
self.assertIn(query, results)