def test_load_coverage(self):
testFile = self.resourceFile("sample_coverage.bed")
ac = ADAMContext(self.sc)
coverage = ac.loadCoverage(testFile)
self.assertEqual(coverage.toDF().count(), 3)
def test_load_coverage(self):
testFile = self.resourceFile("sample_coverage.bed")
ac = ADAMContext(self.ss)
coverage = ac.loadCoverage(testFile)
self.assertEqual(coverage.toDF().count(), 3)
def test_example_coverage(self):
# load file
ac = ADAMContext(self.sc)
testFile = self.exampleFile("chr17.7500000-7515000.sam.coverage.adam")
# read alignments
coverage = ac.loadCoverage(testFile)
qc = CoverageDistribution(self.sc, coverage)
cd1 = qc.plot(testMode=True, cumulative=True)
assert (len(cd1) == 1)
x = cd1.pop()
assert (x[1] == 6)
assert (x[2] == 38)
cd2 = qc.plot(testMode=True, cumulative=False)
assert (len(cd2) == 1)
x = cd2.pop()
assert (x[1] == 6)
assert (x[2] == 32)
cd3 = qc.plot(testMode=True, cumulative=True, normalize=True)
total = float(sum(qc.collectedCoverage[0].values()))
assert (len(cd3) == 1)
x = cd3.pop()
assert (x[1] == 6.0 / total)
assert (x[2] == 38.0 / total)
cd4 = qc.plot(testMode=True, normalize=True)
assert (len(cd4) == 1)
x = cd4.pop()
assert (x[1] == 6.0 / total)
assert (x[2] == 32.0 / total)
