def testPileupMeanOutlierCoverage(self):
"""Verify computation of pileup outlier coverage."""
BCT = BM_coverageType_C()
BCT.type = CT.P_MEAN_OUTLIER
BCT.upperCut = 1.0
BCT.lowerCut = 1.0
pBCT = c.POINTER(BM_coverageType_C)
pBCT = c.pointer(BCT)
coverage = self.CW._estimate_P_MEAN_OUTLIER_Coverage(self.even_c_array, pBCT, len(self.even_list))
lower_bound = mean(self.even_list) - BCT.lowerCut * std(self.even_list)
if lower_bound < 0:
lower_bound = 0
upper_bound = mean(self.even_list) + BCT.upperCut * std(self.even_list)
valid_indices = [i for i, x in enumerate(self.even_list) if (x >= lower_bound and x <= upper_bound)]
np_even_list = array(self.even_list)
assert_equals(coverage, mean(np_even_list[valid_indices]))
coverage = self.CW._estimate_P_MEAN_OUTLIER_Coverage(self.odd_c_array, pBCT, len(self.odd_list))
lower_bound = mean(self.odd_list) - BCT.lowerCut * std(self.odd_list)
if lower_bound < 0:
lower_bound = 0
upper_bound = mean(self.odd_list) + BCT.upperCut * std(self.odd_list)
valid_indices = [i for i, x in enumerate(self.odd_list) if (x >= lower_bound and x <= upper_bound)]
np_odd_list = array(self.odd_list)
assert_equals(coverage, mean(np_odd_list[valid_indices]))
def testPileupMeanTrimmedCoverageInvalidTrim(self):
"""Verify computation of pileup mean trimmed coverage when given an invalid trimming range."""
BCT = BM_coverageType_C()
BCT.type = CT.P_MEAN_TRIMMED
BCT.upperCut = 60.0
BCT.lowerCut = 60.0
pBCT = c.POINTER(BM_coverageType_C)
pBCT = c.pointer(BCT)
coverage = self.CW._estimate_P_MEAN_TRIMMED_Coverage(self.even_c_array, pBCT, len(self.even_list))
assert_true(isnan(coverage))
def testPileupMeanOutlierCoverageZeroStd(self):
"""Verify computation of pileup outlier coverage when given a std of zero."""
BCT = BM_coverageType_C()
BCT.type = CT.P_MEAN_OUTLIER
BCT.upperCut = 0.0
BCT.lowerCut = 0.0
pBCT = c.POINTER(BM_coverageType_C)
pBCT = c.pointer(BCT)
coverage = self.CW._estimate_P_MEAN_OUTLIER_Coverage(self.even_c_array, pBCT, len(self.even_list))
assert_equals(coverage, 0)
def testPileupMeanOutlierCoverageSingle(self):
"""Verify computation of pileup outlier coverage when given an array with a single element."""
BCT = BM_coverageType_C()
BCT.type = CT.P_MEAN_OUTLIER
BCT.upperCut = 1.0
BCT.lowerCut = 1.0
pBCT = c.POINTER(BM_coverageType_C)
pBCT = c.pointer(BCT)
coverage = self.CW._estimate_P_MEAN_OUTLIER_Coverage(self.single_num_c_array, self.pBCT, len(self.single_num_list))
assert_equals(coverage, self.single_num_list[0])
def testPileupMeanTrimmedCoverageInvalidTrim(self):
"""Verify computation of pileup mean trimmed coverage when given an invalid trimming range."""
BCT = BM_coverageType_C()
BCT.type = CT.P_MEAN_TRIMMED
BCT.upperCut = 60.0
BCT.lowerCut = 60.0
pBCT = c.POINTER(BM_coverageType_C)
pBCT = c.pointer(BCT)
coverage = self.CW._estimate_P_MEAN_TRIMMED_Coverage(
self.even_c_array, pBCT, len(self.even_list))
assert_true(isnan(coverage))
def testPileupMeanOutlierCoverageZeroStd(self):
"""Verify computation of pileup outlier coverage when given a std of zero."""
BCT = BM_coverageType_C()
BCT.type = CT.P_MEAN_OUTLIER
BCT.upperCut = 0.0
BCT.lowerCut = 0.0
pBCT = c.POINTER(BM_coverageType_C)
pBCT = c.pointer(BCT)
coverage = self.CW._estimate_P_MEAN_OUTLIER_Coverage(
self.even_c_array, pBCT, len(self.even_list))
assert_equals(coverage, 0)
def testPileupMeanOutlierCoverageSingle(self):
"""Verify computation of pileup outlier coverage when given an array with a single element."""
BCT = BM_coverageType_C()
BCT.type = CT.P_MEAN_OUTLIER
BCT.upperCut = 1.0
BCT.lowerCut = 1.0
pBCT = c.POINTER(BM_coverageType_C)
pBCT = c.pointer(BCT)
coverage = self.CW._estimate_P_MEAN_OUTLIER_Coverage(
self.single_num_c_array, self.pBCT, len(self.single_num_list))
assert_equals(coverage, self.single_num_list[0])
def testPileupMeanTrimmedCoverageUnequalTrim(self):
"""Verify computation of pileup mean trimmed coverage when given an unequal trim percentages."""
BCT = BM_coverageType_C()
BCT.type = CT.P_MEAN_TRIMMED
BCT.upperCut = 10.0
BCT.lowerCut = 20.0
pBCT = c.POINTER(BM_coverageType_C)
pBCT = c.pointer(BCT)
coverage = self.CW._estimate_P_MEAN_TRIMMED_Coverage(self.even_c_array, pBCT, len(self.even_list))
trim_lower = int(BCT.lowerCut/100.0 * len(self.even_list)) + 1
trim_upper = len(self.even_list) - int(BCT.upperCut/100.0 * len(self.even_list)) - 1
assert_equals(coverage, mean(self.even_list[trim_lower:trim_upper]))
def testPileupMeanTrimmedCoverageUnequalTrim(self):
"""Verify computation of pileup mean trimmed coverage when given an unequal trim percentages."""
BCT = BM_coverageType_C()
BCT.type = CT.P_MEAN_TRIMMED
BCT.upperCut = 10.0
BCT.lowerCut = 20.0
pBCT = c.POINTER(BM_coverageType_C)
pBCT = c.pointer(BCT)
coverage = self.CW._estimate_P_MEAN_TRIMMED_Coverage(
self.even_c_array, pBCT, len(self.even_list))
trim_lower = int(BCT.lowerCut / 100.0 * len(self.even_list)) + 1
trim_upper = len(self.even_list) - int(
BCT.upperCut / 100.0 * len(self.even_list)) - 1
assert_equals(coverage, mean(self.even_list[trim_lower:trim_upper]))
def testPileupMeanOutlierCoverageUnequalStd(self):
"""Verify computation of pileup outlier coverage when given unequal standard deviations."""
BCT = BM_coverageType_C()
BCT.type = CT.P_MEAN_OUTLIER
BCT.upperCut = 1.0
BCT.lowerCut = 2.5
pBCT = c.POINTER(BM_coverageType_C)
pBCT = c.pointer(BCT)
coverage = self.CW._estimate_P_MEAN_OUTLIER_Coverage(
self.even_c_array, pBCT, len(self.even_list))
lower_bound = mean(self.even_list) - BCT.lowerCut * std(self.even_list)
if lower_bound < 0:
lower_bound = 0
upper_bound = mean(self.even_list) + BCT.upperCut * std(self.even_list)
valid_indices = [
i for i, x in enumerate(self.even_list)
if (x >= lower_bound and x <= upper_bound)
]
np_even_list = array(self.even_list)
assert_equals(coverage, mean(np_even_list[valid_indices]))
def setup_class(self):
"""Setup class variables before any tests."""
self.even_list = list(range(10))
self.even_c_array = (c.c_uint32 * len(self.even_list))()
self.even_c_array[:] = self.even_list
self.odd_list = list(range(9))
self.odd_c_array = (c.c_uint32 * len(self.odd_list))()
self.odd_c_array[:] = self.odd_list
self.unsorted_list = list(range(9))
random.shuffle(self.unsorted_list)
self.unsorted_c_array = (c.c_uint32 * len(self.unsorted_list))()
self.unsorted_c_array[:] = self.unsorted_list
self.empty_list = []
self.empty_c_array = (c.c_uint32 * len(self.empty_list))()
self.empty_c_array[:] = self.empty_list
self.single_num_list = [10]
self.single_num_c_array = (c.c_uint32 * len(self.single_num_list))()
self.single_num_c_array[:] = self.single_num_list
self.zero_list = [0] * 10
self.zero_c_array = (c.c_uint32 * len(self.zero_list))()
self.zero_c_array[:] = self.zero_list
self.BCT = BM_coverageType_C()
self.BCT.type = CT.C_MEAN
self.BCT.upperCut = 10.0
self.BCT.lowerCut = 10.0
self.pBCT = c.POINTER(BM_coverageType_C)
self.pBCT = c.pointer(self.BCT)
self.CW = CWrapper(UT=True)
