def test_sa(self):
ref_genome = "GTCAACGCATGATCGATACGCATGATCGACCNANCN"
bw = BurrowsWheeler(ref_genome)
wt = WaveletTree(ref_genome)
for i in range(len(ref_genome)):
self.assertEqual(bw.get_sa(i), wt.get_sa(i))
def test_rank(self):
ref_genome = "ACGCATGATCACTAGCTAGCATCGACCNANCN"
bw = BurrowsWheeler(ref_genome)
wt = WaveletTree(ref_genome)
for char in ['A', 'C', 'G', 'T', 'N']:
for i in range(len(ref_genome)):
self.assertEqual(bw.rank(char, i), wt.rank(char, i))
def test_algorithms(self):
ref = "TAGAATCGTTTTTTTTTTATCGACTACNACTACAAAAAAAAATGATCNTACNGTAATTTTTTTTTTTAAAAAAAAAACCCCCCCGGN"
simple = BurrowsWheeler(ref, strategy="Simple")
manber = BurrowsWheeler(ref, strategy="ManberMyers")
kaerkkaeinen = BurrowsWheeler(ref, strategy="KaerkkaeinenSanders")
self.assertEqual(str(simple), str(manber))
self.assertEqual(str(simple), str(kaerkkaeinen))
def test_basic(self):
with self.assertRaises(ValueError):
BurrowsWheeler("")
with self.assertRaises(ValueError):
BurrowsWheeler("A", "A")
with self.assertRaises(ValueError):
BurrowsWheeler("A", strategy="fun")
with self.assertRaises(ValueError):
BurrowsWheeler("A", compression_occ=-1)
with self.assertRaises(ValueError):
BurrowsWheeler("A", compression_sa=-1)
BurrowsWheeler("CACGTACGTGTGCTAACACGTGTGTTTTTGAC")
suffix = BurrowsWheeler("GCAGTN").sa
encoded = BurrowsWheeler("ACGTGTAC").get_bwt("ACGTGTAC")
self.assertIsInstance(encoded, str)
self.assertIsInstance(suffix, list)
string = "ACGATCGATCAGTAC"
self.assertEqual(len(string), len(BurrowsWheeler(string)))
def test_sa_compression(self):
refs = ["TAGAATCGTTTTTTTTTTATCGACTACNACTACAAAAAAAAATGATCNTACNGTAA",
"TTTTTTTTTTTAAAAAAAAAACCCCCCCGGN",
"AGCTA", "T"]
for ref in refs:
for comp in range(1, 50):
for i in range(1, len(ref)):
bw_uncompressed = BurrowsWheeler(ref, compression_occ=1, compression_sa=1)
bw = BurrowsWheeler(ref, compression_occ=1, compression_sa=comp)
self.assertEqual(bw_uncompressed.sa[i], bw.get_sa(i))
def test_encode_decode(self):
string = "NNCACGTACGTGTGCTAACACGTGTGTTTTTGAC"
bwt = BurrowsWheeler(string)
self.assertEqual(str(bwt), string)