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)) )