def __init__(self,
region,
track,
track2,
tail='more',
globalSource='',
minimal=False,
**kwArgs):
if isIter(region):
raise SplittableStatNotAvailableError()
#if minimal == True:
# self._globalSource = MinimalBinSource(region.genome)
#elif globalSource == 'test':
# self._globalSource = UserBinSource('TestGenome:chr21:10000000-15000000','1000000')
#else:
# self._globalSource = GlobalBinSource(region.genome)
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(
globalSource, region.genome, minimal)
assert tail in ['more', 'less', 'different']
self._tail = tail
super(self.__class__, self).__init__(region,
track,
track2,
tail=tail,
globalSource=globalSource,
minimal=minimal,
**kwArgs)
def __init__(self, region, track, track2, tail='more', globalSource='chrs', minimal=False, **kwArgs):
if isIter(region):
raise SplittableStatNotAvailableError()
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(globalSource, region.genome, minimal)
#if minimal == True:
# self._globalSource = MinimalBinSource(region.genome)
#elif globalSource == 'test':
# self._globalSource = UserBinSource('TestGenome:chr21:10000000-15000000','1000000')
#elif globalSource == 'chrs':
# self._globalSource = GenomeInfo.getChrRegs(region.genome)
#elif globalSource == 'chrarms':
# self._globalSource = GenomeInfo.getChrArmRegs(region.genome)
#elif globalSource == 'ensembl':
# self._globalSource = GenomeInfo.getStdGeneRegs(region.genome)
#elif globalSource == 'userbins':
# from gold.application.StatRunner import StatJob
# assert StatJob.USER_BIN_SOURCE is not None
# self._globalSource = StatJob.USER_BIN_SOURCE
# #self._globalSource = kwArgs['userBins']
#else:
# raise ShouldNotOccurError('globalSource not recognized')
# #self._globalSource = GlobalBinSource(region.genome)
assert tail in ['more', 'less', 'different']
self._tail = tail
super(self.__class__, self).__init__(region, track, track2, tail=tail, globalSource=globalSource, minimal=minimal, **kwArgs)
def _init(self,
globalSource='',
kernelType='uniform',
minimal=False,
**kwArgs):
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(
globalSource, self.getGenome(), minimal)
self._kernelType = kernelType
def __init__(self, region, track, track2, tail='more', globalSource='', minimal=False, **kwArgs):
if isIter(region):
raise SplittableStatNotAvailableError()
#if minimal == True:
# self._globalSource = MinimalBinSource(region.genome)
#elif globalSource == 'test':
# self._globalSource = UserBinSource('TestGenome:chr21:10000000-15000000','1000000')
#else:
# self._globalSource = GlobalBinSource(region.genome)
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(globalSource, region.genome, minimal)
assert tail in ['more', 'less', 'different']
self._tail = tail
super(self.__class__, self).__init__(region, track, track2, tail=tail, globalSource=globalSource, minimal=minimal, **kwArgs)
def __init__(self, region, track, track2, tail='more', globalSource='', minimal=False, **kwArgs):
if isIter(region):
# TODO: Introduce a better general mechanism for removing global results. SplittableStatNotAvailableError
# should be exclusive to RawDataStat to minimize confusion.
raise SplittableStatNotAvailableError()
#if minimal == True:
# self._globalSource = MinimalBinSource(region.genome)
#elif globalSource == 'test':
# self._globalSource = UserBinSource('TestGenome:chr21:10000000-15000000','1000000')
#else:
# self._globalSource = GlobalBinSource(region.genome)
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(globalSource, region.genome, minimal)
assert tail in ['more', 'less', 'different']
self._tail = tail
super(self.__class__, self).__init__(region, track, track2, tail=tail, globalSource=globalSource, minimal=minimal, **kwArgs)
def __init__(self,
region,
track,
track2,
tail='more',
globalSource='chrs',
minimal=False,
**kwArgs):
if isIter(region):
raise SplittableStatNotAvailableError()
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(
globalSource, region.genome, minimal)
#if minimal == True:
# self._globalSource = MinimalBinSource(region.genome)
#elif globalSource == 'test':
# self._globalSource = UserBinSource('TestGenome:chr21:10000000-15000000','1000000')
#elif globalSource == 'chrs':
# self._globalSource = GenomeInfo.getChrRegs(region.genome)
#elif globalSource == 'chrarms':
# self._globalSource = GenomeInfo.getChrArmRegs(region.genome)
#elif globalSource == 'ensembl':
# self._globalSource = GenomeInfo.getStdGeneRegs(region.genome)
#elif globalSource == 'userbins':
# from gold.application.StatRunner import StatJob
# assert StatJob.USER_BIN_SOURCE is not None
# self._globalSource = StatJob.USER_BIN_SOURCE
# #self._globalSource = kwArgs['userBins']
#else:
# raise ShouldNotOccurError('globalSource not recognized')
# #self._globalSource = GlobalBinSource(region.genome)
assert tail in ['more', 'less', 'different']
self._tail = tail
super(self.__class__, self).__init__(region,
track,
track2,
tail=tail,
globalSource=globalSource,
minimal=minimal,
**kwArgs)
def _init(self, globalSource=None, minimal=False, **kwArgs):
assert globalSource is not None
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(globalSource, self._region.genome, minimal)
def _init(self, globalSource=None, minimal=False, **kwArgs):
assert globalSource is not None
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(
globalSource, self._region.genome, minimal)
def _createChildren(self):
# ,
self._track._trackFormatReq._allowOverlaps = True
self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(val='category', allowOverlaps=True)) )
#self._addChild( CountPointStat(self._region, self._track, TrackFormatReq(val='category', allowOverlaps=False)) )
self._addChild(ListOfPresentCategoriesStat(GenericRelativeToGlobalStatUnsplittable.getGlobalSource('chrs', self.getGenome(), self._minimal), self._track))
def __init__(self, region, track, track2=None, minimal=False, **kwArgs):
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource('userbins', region.genome, minimal)
super(self.__class__, self).__init__(region, track, track2, minimal=minimal, **kwArgs)
def _init(self, bpWindow='100', minimal=False, **kwArgs):
self._bpWindow = int(bpWindow)
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(
'userbins', self.getGenome(), minimal)
def _init(self, globalSource='', minimal=False, **kwArgs):
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(globalSource, self.getGenome(), minimal)