def test_time_to_read(self):
t = time.perf_counter_ns()
GenomeIndex.read(data_root / "genome.chr22.fa.gz.sa32_index")
t = (time.perf_counter_ns() - t) * 1e-9
# About 30s
self.assertTrue(0 <= t < 300)
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_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 from_files(cls, *, fa, fq1, fq2):
"""
Reference genome file `fa`.
FASTQ files `fq1` and `fq2`.
Creates an instance of AllTheKingsHorses and
yields from its map_paired(...) member function.
"""
ref_genome = unlist1(from_fasta(fa))
index = GenomeIndex.read_or_make(path_to_genome=fa)
aligner = SequenceAligner()
atkh = AllTheKingsHorses(genome_index=index,
sequence_aligner=aligner,
ref_genome=ref_genome)
class _:
headers = atkh.headers()
alignments = atkh.map_paired(fq1, fq2)
return _
def test_read_query(self):
print("read")
index = GenomeIndex.read(data_root / "genome.chr22.fa.gz.sa32_index")
# The following strings are copied from the original genome
ns = 10**(-9)
print(len("AAAAGAATGCA"))
start = time.perf_counter_ns()
self.assertGreater(len(index.query("AAAAGAATGCA")), 0)
end = time.perf_counter_ns()
print("time: ", ns * (end - start))
print(len("CGACACCACCAAGGCCACCCACCTGCCT"))
start = time.perf_counter_ns()
self.assertGreater(len(index.query("CGACACCACCAAGGCCACCCACCTGCCT")), 0)
end = time.perf_counter_ns()
print("time: ", ns * (end - start))
print(
len("GGCATTTACAACTAAAACATTGAATTCAGATTCATTTTCAGGTAATGATATAATCATGTG")
)
start = time.perf_counter_ns()
self.assertGreater(
len(
index.query(
"GGCATTTACAACTAAAACATTGAATTCAGATTCATTTTCAGGTAATGATATAATCATGTG"
)), 0)
end = time.perf_counter_ns()
print("time: ", ns * (end - start))
print(
len("AAAAGAATGCATTTCTGTATTTTTTGAAACCTTTTCTTTTGAAAACATAGTAATACATTT"
"CTACTCTAAAATAGAACTTAGCCTAAATACTTTCAAAACCTTTAGAATTTGGAAAAGAAA")
)
start = time.perf_counter_ns()
self.assertGreater(
len(
index.query(
"AAAAGAATGCATTTCTGTATTTTTTGAAACCTTTTCTTTTGAAAACATAGTAATACATTT"
"CTACTCTAAAATAGAACTTAGCCTAAATACTTTCAAAACCTTTAGAATTTGGAAAAGAAA"
)), 0)
end = time.perf_counter_ns()
print("time: ", ns * (end - start))
print(len("AAAAGAATGCA"))
start = time.perf_counter_ns()
self.assertGreater(len(index.query("AAAAGAATGCA")), 0)
end = time.perf_counter_ns()
print("time: ", ns * (end - start))
print(len("CGACACCACCAAGGCCACCCACCTGCCT"))
start = time.perf_counter_ns()
self.assertGreater(len(index.query("CGACACCACCAAGGCCACCCACCTGCCT")), 0)
end = time.perf_counter_ns()
print("time: ", ns * (end - start))
print(
len("GGCATTTACAACTAAAACATTGAATTCAGATTCATTTTCAGGTAATGATATAATCATGTG")
)
start = time.perf_counter_ns()
self.assertGreater(
len(
index.query(
"GGCATTTACAACTAAAACATTGAATTCAGATTCATTTTCAGGTAATGATATAATCATGTG"
)), 0)
end = time.perf_counter_ns()
print("time: ", ns * (end - start))
print(
len("AAAAGAATGCATTTCTGTATTTTTTGAAACCTTTTCTTTTGAAAACATAGTAATACATTT"
"CTACTCTAAAATAGAACTTAGCCTAAATACTTTCAAAACCTTTAGAATTTGGAAAAGAAA")
)
start = time.perf_counter_ns()
self.assertGreater(
len(
index.query(
"AAAAGAATGCATTTCTGTATTTTTTGAAACCTTTTCTTTTGAAAACATAGTAATACATTT"
"CTACTCTAAAATAGAACTTAGCCTAAATACTTTCAAAACCTTTAGAATTTGGAAAAGAAA"
)), 0)
end = time.perf_counter_ns()
print("time: ", ns * (end - start))