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,
rawStatistic=None,
globalSource='',
minimal=False,
**kwArgs):
if isIter(self._region):
raise SplittableStatNotAvailableError()
self._rawStatistic = self.getRawStatisticClass(rawStatistic)
self._globalSource = GenericRelativeToGlobalStatUnsplittable.getGlobalSource(
globalSource, self._region.genome, minimal)
def _init(self, globalSource='', minimal=False):
if isIter(self._region):
raise SplittableStatNotAvailableError()
if minimal:
self._globalSource = MinimalBinSource(self._region.genome)
elif globalSource == 'test':
self._globalSource = UserBinSource(
'TestGenome:chr21:10000000-15000000', '1000000')
else:
self._globalSource = GlobalBinSource(self._region.genome)
def __init__(self, region, track, track2, 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)
super(self.__class__, self).__init__(region, track, track2, globalSource=globalSource, minimal=minimal, **kwArgs)
def __init__(self,
region,
track,
trackFormatReq=NeutralTrackFormatReq(),
**kwArgs):
if isIter(region):
raise SplittableStatNotAvailableError()
super(self.__class__, self).__init__(region,
track,
trackFormatReq=trackFormatReq,
**kwArgs)
self._track.addFormatReq(trackFormatReq)
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, region, track, **kwArgs):
if hasattr(region, '__iter__'):
raise SplittableStatNotAvailableError()
super(self.__class__, self).__init__(region, track, **kwArgs)
def _init(self, globalSource=None, weightThreshold=None, **kwArgs):
if isIter(self._region):
raise SplittableStatNotAvailableError()
assert globalSource is not None
assert weightThreshold is not None
self._weightThreshold = float(weightThreshold)