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#!/usr/bin/env python
# Time-stamp: <2020-11-24 17:52:13 Tao Liu>
"""Module Description: Test functions to calculate probabilities.
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD License (see the file LICENSE included with
the distribution).
"""
import unittest
from math import log10
from MACS3.Signal.Prob import *
# ------------------------------------
# Main function
# ------------------------------------
class Test_factorial(unittest.TestCase):
def setUp(self):
self.n1 = 100
self.n2 = 10
self.n3 = 1
def test_factorial_big_n1(self):
expect = 9.332622e+157
result = factorial(self.n1)
self.assertTrue( abs(result - expect) < 1e-5*result)
def test_factorial_median_n2(self):
expect = 3628800
result = factorial(self.n2)
self.assertEqual(result, expect)
def test_factorial_small_n3(self):
expect = 1
result = factorial(self.n3)
self.assertEqual(result, expect)
class Test_poisson_cdf(unittest.TestCase):
def setUp(self):
# n, lam
self.n1 = (80,100)
self.n2 = (200,100)
self.n3 = (100,1000)
self.n4 = (1500,1000)
def test_poisson_cdf_n1(self):
expect = (round(0.9773508,5),round(0.02264918,5))
result = (round(poisson_cdf(self.n1[0],self.n1[1],False),5),
round(poisson_cdf(self.n1[0],self.n1[1],True),5))
self.assertEqual( result, expect )
def test_poisson_cdf_n2(self):
expect = (round(log10(4.626179e-19),4),
round(log10(1),4))
result = (round(log10(poisson_cdf(self.n2[0],self.n2[1],False)),4),
round(log10(poisson_cdf(self.n2[0],self.n2[1],True)),4))
self.assertEqual( result, expect )
def test_poisson_cdf_n3(self):
expect = (round(log10(1),2),
round(log10(6.042525e-293),2))
result = (round(poisson_cdf(self.n3[0],self.n3[1],False,True),2),
round(poisson_cdf(self.n3[0],self.n3[1],True,True),2))
self.assertEqual( result, expect )
def test_poisson_cdf_n4(self):
expect = (round(log10(2.097225e-49),4),
round(log10(1),4))
result = (round(log10(poisson_cdf(self.n4[0],self.n4[1],False)),4),
round(log10(poisson_cdf(self.n4[0],self.n4[1],True)),4))
self.assertEqual( result, expect )
class Test_chisq_p_e(unittest.TestCase):
"""Test chisq pvalue calculation -- assuming df is an even number. We
only implemented even number pchisq for upper tail. Because this
is the function we need to combine p-values using fisher's method
"""
def setUp(self):
# x, k, p(upper), -log p upper, -log10 p upper
self.c = ((10, 2, 0.006737947, 5, 2.171472),
(100, 2, 1.92875e-22, 50, 21.71472),
(1000, 22, 1.956374e-197, 452.9382, 196.7085),
(10, 4, 0.04042768, 3.208241, 1.393321),
(100, 8, 4.269159e-18, 39.99511, 17.36966),
(1000, 80, 6.889598e-159, 364.181, 158.1618),
(54, 6, 7.377151e-10, 21.02746, 9.132111),
(565, 10, 5.518772e-115, 263.0891, 114.2582 ),
(7765, 12, 0, 3845.965, 1670.2814),
)
def test_chisq_p(self):
expect = [round(x[2],4) for x in self.c]
result = [round(chisq_pvalue_e(x[0],x[1]),4) for x in self.c]
self.assertEqual( result, expect )
def test_chisq_logp(self):
expect = [round(x[3],4) for x in self.c]
result = [round(chisq_logp_e(x[0],x[1]),4) for x in self.c]
self.assertEqual( result, expect )
def test_chisq_log10p(self):
expect = [round(x[4],4) for x in self.c]
result = [round(chisq_logp_e(x[0],x[1],log10=True),4) for x in self.c]
self.assertEqual( result, expect )
class Test_binomial_cdf(unittest.TestCase):
def setUp(self):
# x, a, b
self.n1 = (20,1000,0.01)
self.n2 = (200,1000,0.01)
def test_binomial_cdf_n1(self):
expect = (round(0.001496482,5),round(0.9985035,5))
result = (round(binomial_cdf(self.n1[0],self.n1[1],self.n1[2],False),5),
round(binomial_cdf(self.n1[0],self.n1[1],self.n1[2],True),5))
self.assertEqual( result, expect )
def test_binomial_cdf_n2(self):
expect = (round(log10(8.928717e-190),4),
round(log10(1),4))
result = (round(log10(binomial_cdf(self.n2[0],self.n2[1],self.n2[2],False)),4),
round(log10(binomial_cdf(self.n2[0],self.n2[1],self.n2[2],True)),4))
self.assertEqual( result, expect )
class Test_binomial_cdf_inv(unittest.TestCase):
def setUp(self):
# x, a, b
self.n1 = (0.1,1000,0.01)
self.n2 = (0.01,1000,0.01)
def test_binomial_cdf_inv_n1(self):
expect = 6
result = binomial_cdf_inv(self.n1[0],self.n1[1],self.n1[2])
self.assertEqual( result, expect )
def test_poisson_cdf_inv_n2(self):
expect = 3
result = binomial_cdf_inv(self.n2[0],self.n2[1],self.n2[2])
self.assertEqual( result, expect )
class Test_binomial_pdf(unittest.TestCase):
def setUp(self):
# x, a, b
self.n1 = (20,1000,0.01)
self.n2 = (200,1000,0.01)
def test_binomial_cdf_inv_n1(self):
expect = round(0.001791878,5)
result = round(binomial_pdf(self.n1[0],self.n1[1],self.n1[2]),5)
self.assertEqual( result, expect )
def test_poisson_cdf_inv_n2(self):
expect = round(log10(2.132196e-188),4)
result = binomial_pdf(self.n2[0],self.n2[1],self.n2[2])
result = round(log10(result),4)
self.assertEqual( result, expect )
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