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)
# print 's=%.4f; p=%.3f' % (stat, p)
stat, p = blockwise_bootstrap(s, ipdft_calc, block_size=10,
num_reps=1000, seq_to_symbols=seq_to_symbol)
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)
