<reponame>oaxiom/NucleoATAC
from unittest import TestCase
import numpy as np
from pyatac.fragmentsizes import FragmentSizes
from nucleoatac.Occupancy import FragmentMixDistribution, calculateOccupancy, OccupancyCalcParams


class Test_occupancy(TestCase):
    """class to test occupancy"""
    def setUp(self):
        """setup Test_occupancy class by establishing parameters"""
        self.fragment_dist = FragmentMixDistribution(0,3)
        self.fragment_dist.nfr_fit = FragmentSizes(0, 3, vals = np.array([0.5, 0.49, 0.01 ]))
        self.fragment_dist.nuc_fit = FragmentSizes(0,3, vals = np.array([0.01, 0.49,0.5]))
        self.params = OccupancyCalcParams(0,3,self.fragment_dist)
    def test_occupancy_calc1(self):
        """test occupancy class for a zero occupancy situation"""
        occ = calculateOccupancy(np.array([1,0,0]),np.array([1,1,1]),self.params)
        self.assertTrue(occ[0] == 0)
    def test_occupancy_calc2(self):
        """test occupancy for a 50% occupancy situation"""
        occ = calculateOccupancy(np.array([1,1,1]),np.array([1,1,1]),self.params)
        self.assertTrue(occ[0] == 0.5)
    def test_occupancy_calc3(self):
        """test average occupancy for when you have 40 random reads,
             which should be 75% from nuc dist
        """
        results = np.zeros(100)
        upper = np.zeros(100)
        lower = np.zeros(100)
        for i in range(100):
            a = np.random.multinomial(10,self.fragment_dist.nfr_fit.get())
            b = np.random.multinomial(30,self.fragment_dist.nuc_fit.get())
            results[i],lower[i],upper[i] = calculateOccupancy(a+b,np.array([1,1,1]),self.params)
        print np.mean(results)
        self.assertTrue(abs(np.mean(results)-0.75)<0.1)
        self.assertTrue(sum(upper < 0.75) < 85)
        self.assertTrue(sum(lower > 0.75) < 85)
    def test_occupancy_calc4(self):
        """test average occupancy for when you have 40 random reads,
             which should be 75% from nuc dist. include some bias
        """
        results = np.zeros(100)
        upper = np.zeros(100)
        lower = np.zeros(100)
        bias = np.array([3,2,1])
        nfrprob = self.fragment_dist.nfr_fit.get() * bias
        nucprob = self.fragment_dist.nuc_fit.get() * bias
        nucprob = nucprob / np.sum(nucprob)
        nfrprob = nfrprob / np.sum(nfrprob)
        for i in range(100):
            a = np.random.multinomial(10,nfrprob)
            b = np.random.multinomial(30,nucprob)
            results[i],lower[i],upper[i] = calculateOccupancy(a+b,bias,self.params)
        print np.mean(results)
        self.assertTrue(abs(np.mean(results)-0.75)<0.1)
        self.assertTrue(sum(upper < 0.75) < 85)
        self.assertTrue(sum(lower > 0.75) < 85)

from unittest import TestCase
import numpy as np
from pyatac.fragmentsizes import FragmentSizes
from nucleoatac.Occupancy import FragmentMixDistribution, calculateOccupancy, OccupancyCalcParams


class Test_occupancy(TestCase):
    """class to test occupancy"""
    def setUp(self):
        """setup Test_occupancy class by establishing parameters"""
        self.fragment_dist = FragmentMixDistribution(0,3)
        self.fragment_dist.nfr_fit = FragmentSizes(0, 3, vals = np.array([0.5, 0.49, 0.01 ]))
        self.fragment_dist.nuc_fit = FragmentSizes(0,3, vals = np.array([0.01, 0.49,0.5]))
        self.params = OccupancyCalcParams(0,3,self.fragment_dist)
    def test_occupancy_calc1(self):
        """test occupancy class for a zero occupancy situation"""
        occ = calculateOccupancy(np.array([1,0,0]),np.array([1,1,1]),self.params)
        self.assertTrue(occ[0] == 0)
    def test_occupancy_calc2(self):
        """test occupancy for a 50% occupancy situation"""
        occ = calculateOccupancy(np.array([1,1,1]),np.array([1,1,1]),self.params)
        self.assertTrue(occ[0] == 0.5)
    def test_occupancy_calc3(self):
        """test average occupancy for when you have 40 random reads,
             which should be 75% from nuc dist
        """
        results = np.zeros(100)
        upper = np.zeros(100)
        lower = np.zeros(100)
        for i in range(100):
            a = np.random.multinomial(10,self.fragment_dist.nfr_fit.get())
            b = np.random.multinomial(30,self.fragment_dist.nuc_fit.get())
            results[i],lower[i],upper[i] = calculateOccupancy(a+b,np.array([1,1,1]),self.params)
        print np.mean(results)
        self.assertTrue(abs(np.mean(results)-0.75)<0.1)
        self.assertTrue(sum(upper < 0.75) < 85)
        self.assertTrue(sum(lower > 0.75) < 85)
    def test_occupancy_calc4(self):
        """test average occupancy for when you have 40 random reads,
             which should be 75% from nuc dist. include some bias
        """
        results = np.zeros(100)
        upper = np.zeros(100)
        lower = np.zeros(100)
        bias = np.array([3,2,1])
        nfrprob = self.fragment_dist.nfr_fit.get() * bias
        nucprob = self.fragment_dist.nuc_fit.get() * bias
        nucprob = nucprob / np.sum(nucprob)
        nfrprob = nfrprob / np.sum(nfrprob)
        for i in range(100):
            a = np.random.multinomial(10,nfrprob)
            b = np.random.multinomial(30,nucprob)
            results[i],lower[i],upper[i] = calculateOccupancy(a+b,bias,self.params)
        print np.mean(results)
        self.assertTrue(abs(np.mean(results)-0.75)<0.1)
        self.assertTrue(sum(upper < 0.75) < 85)
        self.assertTrue(sum(lower > 0.75) < 85)
class to test occupancy setup Test_occupancy class by establishing parameters test occupancy class for a zero occupancy situation test occupancy for a 50% occupancy situation test average occupancy for when you have 40 random reads,              which should be 75% from nuc dist test average occupancy for when you have 40 random reads,              which should be 75% from nuc dist. include some bias