def test_wavelet(self):
ref = "TAGANNGAGATCNGNNNATTNTTTNTCTNNNTGANCTGNACTGACTCAAAAAGN"
for query in ["ACT", "T", "TTT", "TTTT", "GNACT", "AAAA"]:
fm_index = GenomeIndex(ref)
wavelet = GenomeIndex(ref, wavelet=True)
fm_hits = fm_index.query(query)
wavelet_hits = wavelet.query(query)
self.assertEqual(fm_hits, wavelet_hits)
def test_decoding(self):
refs = ["TAGAATCGTTTTTTTTTTATCGACTACNACTACAAAAAAAAATGATCNTACNGTAA",
"TTTTTTTTTTTAAAAAAAAAACCCCCCCGGN",
"AGCTA", "T"]
for ref in refs:
for comp in range(1, 50):
fm_index = GenomeIndex(ref, compression_occ=comp, compression_sa=comp)
self.assertEqual(ref, str(fm_index))
def test_perfect_match_mini(self):
ref = "TAGANNGAGATCNGNNNATTNTTTNTCTNNNTGANCTGNACTGACTCAAAAAGN"
for query in ["ACT", "T", "TTT", "TTTT", "GNACT", "AAAA"]:
fm_index = GenomeIndex(ref)
hits = fm_index.query(query)
# Test for precision
for i in hits:
self.assertEqual(ref[i:(i + len(query))], query)
# Test for recall
from humdum.utils import find_all
self.assertCountEqual(hits, find_all(template=ref, pattern=query))
def test_match_with_compression(self):
ref = "TAGAATCGTTTTTTTTTTATCGACTACNACTACAAAAAAAAATGATCNTACNGTAANNNNNTTNTTTNTCTNNNTGANCTGNACTGACTCAAAAAGN"
for comp in range(1, 100):
fm_index = GenomeIndex(ref, compression_occ=comp, compression_sa=comp + 1)
for query in ["ACT", "T", "TTT", "TTTT", "GNACT", "AAAA"]:
hits = fm_index.query(query)
# Test for precision
for i in hits:
self.assertEqual(ref[i:(i + len(query))], query)
# Test for recall
from humdum.utils import find_all
self.assertCountEqual(hits, find_all(template=ref, pattern=query))
def test_read_write(self):
ref = "NTAGAGNANGACGTACNGATCGANCTGACTNAGCTNNNAGCACACACACTGACTCNNGATCGACNNN"
fm_index = GenomeIndex(ref)
Path(data_root / "index_data").mkdir(parents=True, exist_ok=True)
fm_index.write(data_root / "index_data/index_small.data")
fm_index2 = GenomeIndex.read(data_root / "index_data/index_small.data")
self.assertIsInstance(fm_index2, GenomeIndex)
self.assertEqual(fm_index.bwt.sa, fm_index2.bwt.sa)
self.assertEqual(str(fm_index), str(fm_index2))
self.assertEqual(fm_index.bwt.f, fm_index2.bwt.f)
self.assertEqual(fm_index.bwt.next_chars._data, fm_index2.bwt.next_chars._data)
def test_init_write(self):
genome = ""
with open_maybe_gz(genome_file) as fd:
# skip first line
line = fd.readline()
line = fd.readline().rstrip()
while True:
genome += line
line = fd.readline().rstrip()
if not line:
break
print("length", len(genome))
print("init")
index = GenomeIndex(genome)
print("write")
index.write(data_root / "genome.chr22.fa.gz.sa32_index")
def test_basic(self):
with self.assertRaises(ValueError):
GenomeIndex("ACTG$")
with self.assertRaises(ValueError):
GenomeIndex("$ACTG")
with self.assertRaises(ValueError):
GenomeIndex("#ACTG")
with self.assertRaises(ValueError):
GenomeIndex("")
with self.assertRaises(ValueError):
GenomeIndex("ACGT").query("ACGTTTTTTTTT")
with self.assertRaises(ValueError):
GenomeIndex("ACGT").query("GT$")
with self.assertRaises(ValueError):
GenomeIndex("A", -1)
with self.assertRaises(ValueError):
GenomeIndex("A", compression_occ=-1)
with self.assertRaises(ValueError):
GenomeIndex("A", compression_sa=-1)
self.assertListEqual(GenomeIndex("ATTTTATTTG").query("TTTTTT"), [])
GenomeIndex("A")
GenomeIndex("ACTG")
# Check the type
loc_in_genome = GenomeIndex("NANNTTTTATTTG").query("TTT")
self.assertIsInstance(loc_in_genome, list)
for __ in loc_in_genome:
self.assertIsInstance(__, int)
self.assertCountEqual(GenomeIndex("ATTTTANNTTTTGN").query("TTT"), [1, 2, 8, 9])
def test_constructor(self):
GenomeIndex("ACGT")