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 = WaveletTree(ref, strategy="Simple")
manber = WaveletTree(ref, strategy="ManberMyers")
kaerkkaeinen = WaveletTree(ref, strategy="KaerkkaeinenSanders")
self.assertEqual(str(simple), str(manber))
self.assertEqual(str(simple), str(kaerkkaeinen))
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_sa=1)
bw = WaveletTree(ref, compression_sa=comp)
self.assertEqual(bw_uncompressed.sa[i], bw.get_sa(i))
def test_basic(self):
with self.assertRaises(ValueError):
WaveletTree("")
with self.assertRaises(ValueError):
WaveletTree("A", "A")
with self.assertRaises(ValueError):
WaveletTree("A", strategy="fun")
with self.assertRaises(ValueError):
WaveletTree("A", compression_sa=-1)
WaveletTree("CACGTACGTGTGCTAACACGTGTGTTTTTGAC")
suffix = WaveletTree("GCAGTN").sa
encoded = WaveletTree("ACGTGTAC").get_bwt("ACGTGTAC")
self.assertIsInstance(encoded, str)
self.assertIsInstance(suffix, list)
string = "ACGATCGATCAGTAC"
self.assertEqual(len(string), len(WaveletTree(string)))
def __init__(self,
reference_genome: str,
compression_occ: int = 32,
compression_sa: int = 32,
wavelet=True):
if compression_occ < 1 or compression_sa < 1:
raise ValueError("compression coefficients need to be >=1")
self.__string_checks(reference_genome)
self.compression_occ = compression_occ
self.n = len(reference_genome)
reference_genome += "$"
if wavelet:
self.bwt = WaveletTree(reference_genome,
compression_sa=compression_sa)
else:
self.bwt = BurrowsWheeler(reference_genome,
compression_occ=compression_occ,
compression_sa=compression_sa)
def test_encode_decode(self):
string = "NNCACGTACGTGTGCTAACACGTGTGTTTTTGAC"
bwt = WaveletTree(string)
self.assertEqual(str(bwt), string)