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)