def testReadBigWigChromsomeException(self):
"""
Test for catching bad chromosome names.
"""
continuousObj = continuous.BigWigDataSource(self._bigWigFile)
generator = continuousObj.bigWigToProtocol(
"chr&19", 49305602, 49308000)
next(generator)
def testReadBigWig(self):
continuousObj = continuous.BigWigDataSource(self._bigWigFile)
generator = continuousObj.bigWigToProtocol("chr19", 49305897, 49306090)
tuples = self.getTuples(generator)
self.assertEqual(tuples[0], (49305900, 20.0))
self.assertEqual(tuples[4], (49305904, 20.0))
self.assertEqual(tuples[5], (49306080, 17.5))
self.assertEqual(tuples[9], (49306084, 17.5))
self.assertEqual(len(tuples), 10)
def testReadBigWigNegativeReferenceRange(self):
continuousObj = continuous.BigWigDataSource(self._bigWigFile)
generator = continuousObj.bigWigToProtocol("chr19", -1, 5)
tuples = self.getTuples(generator)
self.assertEqual(len(tuples), 0)
def testReadBigWigOutsideReferenceRange(self):
continuousObj = continuous.BigWigDataSource(self._bigWigFile)
generator = continuousObj.bigWigToProtocol(
"chr19", 49306897, 493059304)
tuples = self.getTuples(generator)
self.assertEqual(len(tuples), 5)
def testReadBigWigInvalidRange(self):
continuousObj = continuous.BigWigDataSource(self._bigWigFile)
generator = continuousObj.bigWigToProtocol(
"chr19", 493059030, 49305934)
next(generator)
def testReadBigWigAllNan(self):
continuousObj = continuous.BigWigDataSource(self._bigWigFile)
generator = continuousObj.bigWigToProtocol(
"chr19", 49305927, 49305997)
tuples = self.getTuples(generator)
self.assertEqual(len(tuples), 0)
