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from unittest import TestCase
import numpy
from numpy.testing import assert_allclose, assert_equal
from cogent3.maths.period import AutoCorrelation, Hybrid, Ipdft, ipdft
from cogent3.maths.stats.period import (
SeqToSymbols,
blockwise_bootstrap,
chi_square,
circular_indices,
factorial,
g_statistic,
seq_to_symbols,
)
class TestPeriodStat(TestCase):
def setUp(self):
x = [
1,
0,
1,
0,
1,
0,
0,
0,
0,
1,
1,
0,
0,
0,
1,
0,
1,
0,
0,
1,
0,
1,
0,
0,
1,
0,
0,
0,
0,
1,
1,
1,
0,
1,
0,
0,
0,
0,
1,
0,
1,
1,
1,
1,
0,
0,
0,
1,
1,
0,
1,
1,
1,
0,
0,
0,
1,
1,
1,
1,
1,
1,
1,
0,
0,
1,
0,
0,
1,
0,
0,
0,
0,
1,
0,
1,
1,
1,
1,
1,
1,
0,
0,
1,
1,
1,
0,
0,
0,
0,
1,
1,
0,
0,
0,
0,
1,
1,
0,
1,
0,
1,
1,
0,
1,
0,
0,
0,
1,
0,
0,
0,
1,
0,
0,
0,
0,
1,
1,
1,
0,
1,
0,
1,
0,
1,
1,
1,
0,
0,
1,
1,
0,
1,
0,
1,
0,
0,
0,
1,
0,
0,
0,
0,
1,
1,
1,
0,
0,
0,
]
self.x = numpy.array(x)
self.sig = numpy.array(self.x, numpy.float64)
self.motifs = ["AA", "TT", "TA"]
def test_chi_square(self):
D, cs_p_val = chi_square(self.x, 10)
self.assertEqual(f"{D:.4f}", "0.4786")
self.assertEqual(f"{cs_p_val:.4f}", "0.4891")
def test_factorial(self):
self.assertEqual(factorial(1), 1)
self.assertEqual(factorial(4), 24)
self.assertEqual(factorial(0), 1)
def test_g_statitic(self):
"""calc g-stat correctly"""
X, periods = ipdft(self.sig, llim=2, ulim=39)
g_obs, p_val = g_statistic(X)
assert_allclose(p_val, 0.9997, rtol=1e-3)
assert_allclose(g_obs, 0.0577, rtol=1e-3)
def test_circular_indices(self):
v = list(range(10))
self.assertEqual(circular_indices(v, 8, 10, 4), [8, 9, 0, 1])
self.assertEqual(circular_indices(v, 9, 10, 4), [9, 0, 1, 2])
self.assertEqual(circular_indices(v, 4, 10, 4), [4, 5, 6, 7])
def test_seq_to_symbol(self):
"""both py and pyx seq_to_symbol versions correctly convert a sequence"""
motifs = [b"AA", b"AT", b"TT"]
symbols = seq_to_symbols(b"AATGGTTA", motifs, 2)
assert_equal(symbols, numpy.array([1, 1, 0, 0, 0, 1, 0, 0]))
symbols = seq_to_symbols(b"AAGATT", motifs, 2, numpy.zeros(6, numpy.uint8))
assert_equal(symbols, numpy.array([1, 0, 0, 1, 1, 0]))
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(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
)
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
)
# print 's=%s; p=%s' % (stat, p)
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.get_num_stats(), 1)
self.assertEqual(ipdft_calc.get_num_stats(), 1)
self.assertEqual(autocorr_calc.get_num_stats(), 1)
hybrid_calc = Hybrid(150, llim=2, period=4, return_all=True)
self.assertEqual(hybrid_calc.get_num_stats(), 3)
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)
|
