def testIntervalStats_OneVsOne(self, chrLenFile, tracks):
method = IntervalStats()
method.setQueryTrackFileNames([tracks[0]])
method.setReferenceTrackFileNames([tracks[1]])
method.setChromLenFileName(chrLenFile)
method.setManualParam('o', 'output')
runAllMethods([method])
self._assertMethodResultsSize(1, method)
def testGiggle_OneVsMany_header_in_data(self, chrLenFile, tracks):
method = Giggle()
method.setQueryTrackFileNames([tracks[6]])
refTracks = [tracks[7], tracks[8]]
method.setReferenceTrackFileNames(refTracks)
# method = MultiMethod(Giggle, [tracks[8]], refTracks)
method.setChromLenFileName(chrLenFile)
runAllMethods([method])
self._printResultFiles(method, ['stderr', 'stdout', 'output'])
self._assertMethodResultsSize(len(refTracks), method)
def testGenometriCorr_OneVsOne_header_in_data(self, chrLenFile, tracks):
# raise Exception('With current setup, too long running time to function as unit test')
method = GenometriCorr()
method.setQueryTrackFileNames([tracks[6]])
method.setReferenceTrackFileNames([tracks[7]])
method.setChromLenFileName(chrLenFile)
method.setManualParam('ecdfPermNum', 5)
method.setManualParam('meanPermNum', 5)
method.setManualParam('jaccardPermNum', 5)
runAllMethods([method])
# self._printResultFiles(method, ['stderr', 'stdout', 'output'])
self._assertMethodResultsSize(1, method)
def testStereoGene_OneVsMany(self, chrLenFile, tracks):
refTracks = [tracks[0], tracks[1]]
qTracks = [tracks[2]]
method = MultiMethod(StereoGene, qTracks, refTracks)
method.setChromLenFileName(chrLenFile)
method.setManualParam('v', True)
method.setManualParam('silent', 0)
method.setManualParam('wSize', 20)
method.setManualParam('bin', 5)
method.setManualParam('kernelSigma', 10.0)
runAllMethods([method])
# self._printResultFiles(method, ['stderr', 'stdout', 'output'])
self._assertMethodResultsSize(2, method)
def testStereoGene_OneVsOne_header_in_data(self, chrLenFile, tracks):
method = StereoGene()
method.setQueryTrackFileNames([tracks[6]])
method.setReferenceTrackFileNames([tracks[7]])
method.setChromLenFileName(chrLenFile)
method.setManualParam('v', True)
method.setManualParam('silent', 0)
method.setManualParam('wSize', 20)
method.setManualParam('bin', 5)
method.setManualParam('kernelSigma', 10.0)
runAllMethods([method])
# self._printResultFiles(method, ['stderr', 'stdout', 'output'])
self._assertMethodResultsSize(1, method)
def _checkThatRuns(self, queryTrack, refTracks, selectionValues,
methodClasses):
workingMethodObjects = WorkingMethodObjectParser(
queryTrack, refTracks, selectionValues,
methodClasses).getWorkingMethodObjects()
runAllMethods(workingMethodObjects)
for wmo in workingMethodObjects:
if PRINT_RESULT_FILES:
self._printResultFiles(wmo, ['stderr', 'stdout', 'output'])
testStat = wmo.getTestStatistic()
pval = wmo.getPValue()
if PRINT_TEST_STATISTICS:
print('TestStat ', wmo.getMethodName(), ': ', testStat)
def testGoShifter_header_in_data(self, chrLenFile, tracks):
method = GoShifter()
# snpmap = pkg_resources.resource_filename('pycolocstats', '../../tests/resources/snpmap.tabular')
# annotation = pkg_resources.resource_filename('pycolocstats', '../../tests/resources/annotation.bed.gz')
# proxies = pkg_resources.resource_filename('pycolocstats', '../../tests/resources/proxies.txt')
method.setQueryTrackFileNames([tracks[9]])
method.setReferenceTrackFileNames([tracks[5]])
# method.setManualParam('s', snpmap)
# method.setManualParam('a', annotation)
method.setManualParam('l', '/root/goshifter/hg38_eur/')
method.setManualParam('p', 10)
method.setManualParam('o', 'output')
runAllMethods([method])
self._printResultFiles(method, ['stderr', 'stdout', 'output'])
self._assertMethodResultsSize(1, method)
def testIntervalStats_OneVsMany(self, chrLenFile, tracks):
method = MultiMethod(IntervalStats, [tracks[0]], tracks[1:3])
method.setChromLenFileName(chrLenFile)
method.setManualParam('o', 'output')
runAllMethods([method])
self._assertMethodResultsSize(2, method)