def test_seq_to_symbol_factory(self):
"""checks factory function for conversion works"""
motifs = ["AA", "AT", "TT"]
seq_to_symbols = SeqToSymbols(motifs)
got = seq_to_symbols("AATGGTTA")
assert_equal(got, numpy.array([1, 1, 0, 0, 0, 1, 0, 0]))
got = seq_to_symbols("AAGATT")
assert_equal(got, numpy.array([1, 0, 0, 1, 1, 0], numpy.uint8))
def test_permutation_all(self):
"""performs permutation test of Hybrid, but considers all stats"""
s = ("ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG"
"GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT"
"AATTTTTAACCGCGGAATTGCGTC")
seq_to_symbol = SeqToSymbols(self.motifs, length=len(s))
hybrid_calc = Hybrid(len(s), period=4, return_all=True)
stat, p = blockwise_bootstrap(s,
hybrid_calc,
block_size=10,
num_reps=1000,
seq_to_symbols=seq_to_symbol)
def test_permutation_skips(self):
"""permutation test correctly handles data without symbols"""
s = "N" * 150
seq_to_symbol = SeqToSymbols(self.motifs, length=len(s))
ipdft_calc = Ipdft(len(s), llim=2, period=4)
stat, p = blockwise_bootstrap(
s,
ipdft_calc,
block_size=10,
num_reps=1000,
seq_to_symbols=seq_to_symbol,
num_stats=1,
)
self.assertEqual(stat, 0.0)
self.assertEqual(p, 1.0)
def test_permutation(self):
s = (
"ATCGTTGGGACCGGTTCAAGTTTTGGAACTCGCAAGGGGTGAATGGTCTTCGTCTAACGCTGG"
"GGAACCCTGAATCGTTGTAACGCTGGGGTCTTTAACCGTTCTAATTTAACGCTGGGGGGTTCT"
"AATTTTTAACCGCGGAATTGCGTC"
)
seq_to_symbol = SeqToSymbols(self.motifs, length=len(s))
hybrid_calc = Hybrid(len(s), llim=2, period=4)
ipdft_calc = Ipdft(len(s), llim=2, period=4)
stat, p = blockwise_bootstrap(
s, hybrid_calc, block_size=10, num_reps=1000, seq_to_symbols=seq_to_symbol
)
stat, p = blockwise_bootstrap(
s, ipdft_calc, block_size=10, num_reps=1000, seq_to_symbols=seq_to_symbol
)