def _createChildren(self):
self._addChild(RawOverlapStat(self._region, self._track, self._track2))
self._addChild(
FormatSpecStat(self._region, self._track,
TrackFormatReq(dense=False, interval=True)))
self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(dense=False, interval=True)))
def _createChildren(self):
self._rawOverlap = self._addChild(
RawOverlapStat(self._region, self._track, self._track2))
self._segmentCoverProportion = self._addChild(
ProportionCountStat(self._region, self._track2))
self._addChild(
FormatSpecStat(self._region, self._track,
TrackFormatReq(dense=False, interval=False)))
self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(dense=False, interval=True)))
def _createChildren(self):
"Takes three tracks: "
t1, t2, t3 = self._tracks
#print 'TEMP4: ',self._kernelType
if self._kernelType == 'uniform':
from quick.statistic.StatFacades import TpRawOverlapStat
self._t2vst1 = self._addChild(
TpRawOverlapStat(self._region, t2, t1, **self._kwArgs))
self._t3vst1 = self._addChild(
SumInsideStat(self._region, t1, t3, **self._kwArgs))
elif self._kernelType == 'binSizeNormalizedV3':
#from quick.statistic.TpProportionOverlapPerBinAvgStat import TpProportionOverlapPerBinAvgStat
#from quick.statistic.MeanInsidePerBinAvgStat import MeanInsidePerBinAvgStat
from quick.statistic.AggregateOfCoveredBpsInSegmentsStat import AggregateOfCoveredBpsInSegmentsStat
from quick.statistic.AggregateOfCoverageInSegmentsStat import AggregateOfCoverageInSegmentsStat
#self._t2vst1 = self._addChild( TpProportionOverlapPerBinAvgStat(self._region, t2,t1, **self._kwArgs))
self._t2vst1 = self._addChild(
AggregateOfCoverageInSegmentsStat(self._region,
t2,
t1,
method='sum_of_mean',
**self._kwArgs))
#self._t3vst1 = self._addChild( MeanInsidePerBinAvgStat(self._region, t1,t3, **self._kwArgs))
self._t3vst1 = self._addChild(
AggregateOfCoveredBpsInSegmentsStat(self._region,
t3,
t1,
method='sum_of_mean',
**self._kwArgs))
if self._kwArgs.get('useNormalizedTestStatistic') == 'yes':
from gold.statistic.CountSegmentStat import CountSegmentStat
from gold.statistic.SumStat import SumStat
self._globalT2CoverageStat = self._addChild(
CountSegmentStat(self._region, t2, **self._kwArgs))
self._globalT3CoverageStat = self._addChild(
SumStat(self._region, t3, **self._kwArgs))
else:
#self._t2vst1 = self._addChild( KernelWeightedT1SegsInTpRawOverlapStat(self._region, t1,t2, **self._kwArgs))
self._t2vst1 = self._addChild(
KernelWeightedT1SegsInTpRawOverlapVersion2Stat(
self._globalSource, t1, t2, **self._kwArgs))
self._t3vst1 = self._addChild(
KernelWeightedSumInsideStat(self._globalSource, t3, t1,
**self._kwArgs))
self._addChild(
FormatSpecStat(self._region, t1,
TrackFormatReq(allowOverlaps=False)))
self._addChild(
FormatSpecStat(self._region, t2,
TrackFormatReq(allowOverlaps=False)))
def _createChildren(self):
kwArgs = copy(self._kwArgs)
if 'rawStatistic' in kwArgs:
del kwArgs['rawStatistic']
self._addChild(
FormatSpecStat(self._region, self._track,
TrackFormatReq(dense=False, val='category')))
self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(dense=False, val='tc')))
self._addChild(
self._rawStatistic(self._region, self._track, self._track2,
**kwArgs))
def _createChildren(self):
self._addChild(BpLevelArrayRawDataStat(self._region, self._track))
self._addChild(BpLevelArrayRawDataStat(self._region, self._track2))
allowOverlaps = self._configuredToAllowOverlaps(
strict=False, allowReturningNone=True)
self._addChild(
FormatSpecStat(
self._region, self._track,
TrackFormatReq(dense=False, allowOverlaps=allowOverlaps)))
self._addChild(
FormatSpecStat(
self._region, self._track2,
TrackFormatReq(dense=False, allowOverlaps=allowOverlaps)))
def _createChildren(self):
from quick.statistic.StatFacades import TpRawOverlapStat
t1, t2, t3 = self._tracks
from gold.statistic.MeanInsideStat import SumInsideStat
self._t2vst1 = self._addChild(
TpRawOverlapStat(self._region, t2, t1, **self._kwArgs))
self._t3vst1 = self._addChild(
SumInsideStat(self._region, t1, t3, **self._kwArgs))
self._addChild(
FormatSpecStat(self._region, t1,
TrackFormatReq(allowOverlaps=False)))
self._addChild(
FormatSpecStat(self._region, t2,
TrackFormatReq(allowOverlaps=False)))
def _createChildren(self):
self._addChild(
PointCountInsideSegsStat(self._region, self._track, self._track2))
self._addChild(CountStat(self._region, self._track2))
self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(dense=False, interval=True)))
def _createChildren(self):
self._graphStat = self._addChild(GraphStat(self._region, self._track))
self._position2NodeId = self._addChild(
PositionToGraphNodeIdStat(self._region, self._track, self._track2))
dummyStat = self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(allowOverlaps=False)))
def _createChildren(self):
kwArgs = copy(self._kwArgs)
if 'rawStatistic' in kwArgs:
del kwArgs['rawStatistic']
track2 = self._track2 if hasattr(self, '_track2') else None
self._addChild(
FormatSpecStat(self._region, self._track,
TrackFormatReq(dense=False, val='tc')))
#self._track.formatConverters = 'Dummy' #to avoid check of tracks not being used..
#self._track2.formatConverters = 'Dummy' #to avoid check of tracks not being used..
#self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(dense=False, val='tc') ) )
self._addChild(
self._rawStatistic(
self._region, self._track, track2, **
kwArgs)) #This will actually compute, without any use for it.
self._indexOfFirstSubCatChild = len(self._children)
for subtype1 in ['0', '1']:
#for subtype2 in ['0','1']:
tn1 = self._track.trackName + [subtype1]
if not os.path.exists(createDirPath(tn1, self.getGenome())):
#logMessage('DID NOT EXIST.. '+createOrigPath(self.getGenome(),tn1))
raise IncompatibleTracksError
#else:
# logMessage('DID EXIST')
track1 = Track(tn1)
track1.formatConverters = self._track.formatConverters
#track2 = Track( self._track2.trackName + [subtype2])
#track2.formatConverters = self._track2.formatConverters
self._addChild(
self._rawStatistic(self._region, track1, track2, **kwArgs))
def _createChildren(self):
#self._track provide intervals for inside vs outside, self._track2 provide values
sumInsideStat = SumInsideStat(self._region, self._track, self._track2)
countInsideStat = CountStat(self._region, self._track)
#sumAllStat = SumStat(self._region, self._track2)
sumAllStat = SumOverCoveredBpsStat(self._region, self._track2)
countAllStat = CountStat(self._region, self._track2)
self._addChild(sumInsideStat)
self._addChild(countInsideStat)
self._addChild(sumAllStat)
self._addChild(countAllStat)
from config.Config import IS_EXPERIMENTAL_INSTALLATION
if not IS_EXPERIMENTAL_INSTALLATION:
self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(dense=True)))
def _createChildren(self):
self._valBpArrayStat = self._addChild(
ValueBpLevelArrayRawDataStat(self._region,
self._track,
voidValue=0))
self._addChild(
FormatSpecStat(self._region, self._track,
TrackFormatReq(allowOverlaps=False, val='number')))
self._segmentBpArrayStat = self._addChild(
BpLevelArrayRawDataStat(self._region,
self._track2,
bpDepthType='binary'))
self._segStat = self._addChild(
RawDataStat(
self._region, self._track2,
TrackFormatReq(allowOverlaps=False, dense=False,
interval=True)))
def _createChildren(self):
from quick.statistic.StatFacades import TpRawOverlapStat
t1,t2,t3 = self._tracks
if self._configuredToAllowOverlaps(strict=False):
self._t2vst1 = self._addChild( TpRawOverlapAllowSingleTrackOverlapsStat(self._region, t2,t1))
self._t3vst1 = self._addChild( TpRawOverlapAllowSingleTrackOverlapsStat(self._region, t3,t1))
self._addChild( FormatSpecStat(self._region, t1, TrackFormatReq(allowOverlaps=True)) )
self._addChild( FormatSpecStat(self._region, t2, TrackFormatReq(allowOverlaps=True)) )
self._addChild( FormatSpecStat(self._region, t3, TrackFormatReq(allowOverlaps=True)) )
elif self._kwArgs.get('onlyT3WithOverlap') == 'yes':
#self._t2vst1 = self._addChild( TpRawOverlapAllowSingleTrackOverlapsStat(self._region, t2,t1, **self._kwArgs))
self._t2vst1 = self._addChild( TpRawOverlapStat(self._region, t2,t1, **self._kwArgs))
self._t3vst1 = self._addChild( TpRawOverlapAllowSingleTrackOverlapsStat(self._region, t3,t1, **self._kwArgs))
self._addChild( FormatSpecStat(self._region, t1, TrackFormatReq(allowOverlaps=False)) )
self._addChild( FormatSpecStat(self._region, t2, TrackFormatReq(allowOverlaps=False)) )
self._addChild( FormatSpecStat(self._region, t3, TrackFormatReq(allowOverlaps=True)) )
else:
self._t2vst1 = self._addChild( TpRawOverlapStat(self._region, t2,t1))
self._t3vst1 = self._addChild( TpRawOverlapStat(self._region, t3,t1))
def _createChildren(self):
self._addChild(PointGapsStat(self._region, self._track))
self._addChild(
FormatSpecStat(self._region, self._track,
TrackFormatReq(dense=False, interval=False)))
def _createChildren(self):
self._subgraph = self._addChild(
SubMatrixStat(self._region, self._track, self._track2))
requirement = self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(allowOverlaps=False)))
def _createChildren(self):
self._addChild(SumInsideStat(self._region, self._track, self._track2))
self._addChild(CountStat(self._region, self._track))
self._addChild(
FormatSpecStat(self._region, self._track2,
TrackFormatReq(interval=False, dense=False)))
def _createChildren(self):
self._graphStat = self._addChild(
GraphStat(self._region, self._track, isDirected='True'))
self._addChild(
FormatSpecStat(self._region, self._track,
TrackFormatReq(weights='number')))
def _createChildren(self):
#GeneralOneTrackIterateValsStatUnsplittable._createChildren(self)
self._addChild(
FormatSpecStat(self._region, self._track,
TrackFormatReq(val='category')))
def _createChildren(self):
self._addChild( DiscreteMarksStat(self._region, self._track, self._track2, numDiscreteVals=self._numDiscreteVals, printIntervals=True) )
self._addChild( SimpleDiscreteMarksIntensityStat(self._region, self._track, self._track2, numDiscreteVals=self._numDiscreteVals) )
self._addChild( FormatSpecStat(self._region, self._track2, TrackFormatReq(dense=False, interval=False)) )