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(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_get_num_stats(self):
"""calculators should return correct num stats"""
hybrid_calc = Hybrid(150, llim=2, period = 4)
ipdft_calc = Ipdft(150, llim=2, period = 4)
autocorr_calc = AutoCorrelation(150, llim=2, period = 4)
self.assertEqual(hybrid_calc.getNumStats(), 1)
self.assertEqual(ipdft_calc.getNumStats(), 1)
self.assertEqual(autocorr_calc.getNumStats(), 1)
hybrid_calc = Hybrid(150, llim=2, period = 4, return_all=True)
self.assertEqual(hybrid_calc.getNumStats(), 3)