def testSlice(self):
m = self._m
sm = self._sm
AssertList(m[0:0], sm[0:0], self.assertEqual)
AssertList(m[0:100], sm[0:100], self.assertEqual)
AssertList(m[10:20], sm[10:20], self.assertEqual)
AssertList(m[90:110], sm[90:110], self.assertEqual)
AssertList(m[110:120], sm[110:120], self.assertEqual)
def _assertTVEqual(self, target, other):
self.assertEqual(target.genomeAnchor, other.genomeAnchor)
self.assertEqual(target.trackFormat, other.trackFormat)
AssertList([el.start() for el in target],
[el.start() for el in other], self.assertEqual)
AssertList([el.end() for el in target],
[el.end() for el in other], self.assertEqual)
AssertList([el.val() for el in target],
[el.val() for el in other], self.assertAlmostEqual)
AssertList([el.strand() for el in target],
[el.strand() for el in other], self.assertEqual)
def _assertSplitUserBin(self, compBins, start, end):
region = GenomeRegion('hg18', 'chr1', start, end)
compBinRegions = [
GenomeRegion('hg18', 'chr1', elStart, elEnd)
for elStart, elEnd in compBins
]
AssertList(compBinRegions, CompBinManager.splitUserBin(region),
self.assertEqual)
def _assertSlicing(self, i, j):
AssertList([x + 1 for x in self._array[i:j]], self._vpe[i:j],
self.assertEqual)
def testIndexing(self):
AssertList([x + 1 for x in self._array], self._vpe, self.assertEqual)
def _assertIndexFile(self, contents, prefix):
fn = self.path + os.sep + prefix + '.int32'
self.assertTrue(os.path.exists(fn))
fileContents = [el for el in memmap(fn, 'int32', mode='r')]
AssertList(contents, fileContents, self.assertEqual)
def _assertSlide(self, targetWindows, windowSize, source):
windows = SlidingWindow(source, windowSize)
self.assertEqual(len(targetWindows), len([el for el in windows]))
for i, window in enumerate(windows):
AssertList(targetWindows[i], window, self.assertEqual)
def _assertList(self, target, other):
AssertList(target, other, self.assertEqual)