def _createChildren(self): self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(dense=True, val='char'))) self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(val='category')))
def _createChildren(self): self._addChild(RawDataStat(self._region, self._track, \ TrackFormatReq(dense=False, interval=False, \ val='category', allowOverlaps=True))) self._addChild(RawDataStat(self._region, self._track2, \ TrackFormatReq(dense=False, interval=True, \ val='category', allowOverlaps=True)))
def _createChildren(self): self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(interval=True, val=self._markReq))) self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(dense=False, interval=True)))
def _createChildren(self): self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(val='number', dense=True))) self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(val='number', dense=True)))
def _createChildren(self): self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(allowOverlaps=False, val='number'))) self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(allowOverlaps=False, dense=False)))
def _createChildren(self): self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(dense=False, interval=True)) ) #interval=False is supported through the faster PointCountPerSegStat.. self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(dense=False, interval=True)))
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._addChild( RawDataStat( self._region, self._track, TrackFormatReq(dense=False, interval=False, val='number'))) self._addChild( RawDataStat( self._region, self._track2, TrackFormatReq(dense=False, interval=False, val='number')))
def _createChildren(self): rawDataStat = RawDataStat(self._region, self._track, TrackFormatReq(dense=False, interval=False)) self._addChild(rawDataStat) rawDataStat2 = RawDataStat(self._region, self._track2, TrackFormatReq(dense=False, interval=True)) self._addChild(rawDataStat2) self._binSizeStat = self._addChild( BinSizeStat(self._region, self._track2))
def _createChildren(self): rawSegDataStat = RawDataStat( self._region, self._track, TrackFormatReq(interval=True, dense=False)) rawNumDataStat = RawDataStat( self._region, self._track2, TrackFormatReq(dense=True, val='number', interval=False)) self._addChild(rawSegDataStat) self._addChild(rawNumDataStat)
def _createChildren(self): self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(dense=False))) self._addChild( RawDataStat(self._region, self._track2, TrackFormatReq(dense=False))) self._binSizeStat = self._addChild( BinSizeStat(self._region, self._track2))
def _createChildren(self): self._graphNodeIdStat = self._addChild( RawDataStat(self._region, self._track, TrackFormatReq(interval=True, id=True, dense=True))) #self._segmentsStat = self._addChild(RawDataStat(self._region, self._track2, TrackFormatReq(interval=False, dense=False))) self._segmentsStat = self._addChild( RawDataStat( self._region, self._track2, TrackFormatReq(interval=False, dense=False, allowOverlaps=None)))
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 _init(self, scriptFn='', randomSeed=None, **kwArgs): self._trackFormat1 = TrackFormatReq() self._trackFormat2 = TrackFormatReq() self._codeLines = [] if scriptFn != '': self._parseScriptFile(scriptFn.decode('hex_codec')) from gold.util.RandomUtil import getManualSeed, setManualSeed if randomSeed is not None and randomSeed != 'Random' and getManualSeed( ) is None: setManualSeed(int(randomSeed))
def _createChildren(self): #the settings of allowOverlaps is somewhat arbitrary for now.. self._addChild( RawDataStat( self._region, self._track, TrackFormatReq(dense=False, interval=True, allowOverlaps=False))) self._addChild( RawDataStat( self._region, self._track2, TrackFormatReq(dense=False, interval=True, allowOverlaps=False)))
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 testCompatibilityWithExceptions(self): tf = TrackFormat.createInstanceFromPrefixList(['start', 'val'], 'float64', 1, 'float64', 1) self.assertFalse(TrackFormatReq(interval=True, strand=True, val='number')\ .isCompatibleWith(tf)) self.assertFalse(TrackFormatReq(interval=True, strand=True, val='number')\ .isCompatibleWith(tf, ['interval'])) self.assertTrue(TrackFormatReq(interval=True, strand=True, val='number')\ .isCompatibleWith(tf, ['interval', 'hasStrand'])) self.assertFalse(TrackFormatReq(interval=True, strand=True, val='tc')\ .isCompatibleWith(tf, ['interval', 'hasStrand']))
def _parseScriptFile(self, scriptFn): script = open(scriptFn) for line in script: if line.lower().startswith('#format1:'): format = line.replace('#format1:', '').strip() self._trackFormat1 = TrackFormatReq(name=format) elif line.lower().startswith('#format2:'): format = line.replace('#format2:', '').strip() self._trackFormat2 = TrackFormatReq(name=format) elif line[0] == '#': pass else: self._codeLines.append(line.strip())
def _createChildren(self): self._addChild( RawDataStat( self._region, self._track, TrackFormatReq(val='number', allowOverlaps=self._configuredToAllowOverlaps( strict=False)))) self._addChild( RawDataStat( self._region, self._track2, TrackFormatReq(interval=True, allowOverlaps=self._configuredToAllowOverlaps( strict=False))))
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): 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): 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): 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._addChild( RawDataStat( self._region, self._track, TrackFormatReq(allowOverlaps=self._configuredToAllowOverlaps( strict=False)))) pass
def _createChildren(self): rawDataStat = RawDataStat( self._region, self._track, TrackFormatReq(dense=False, interval=False, allowOverlaps=(self._withOverlaps == 'yes'))) self._addChild(rawDataStat)
def _createChildren(self): for track in self._tracks: self._addChild( RawDataStat(self._region, track, TrackFormatReq(dense=False), **self._kwArgs)) self._binSizeStat = self._addChild( BinSizeStat(self._region, self._tracks[0]))
def _createChildren(self): self._addChild( RawDataStat( self._region, self._track, TrackFormatReq(interval=True, val='category', allowOverlaps=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): 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 _combineTrackTypeVals(self, curVal, nextVal): try: return self._combineEqualVals(curVal, nextVal) except InvalidFormatError: from gold.track.TrackFormat import TrackFormatReq curReq = TrackFormatReq(name=curVal) nextReq = TrackFormatReq(name=nextVal) maxCommonCoreType = TrackFormatReq.maxCommonCoreFormat( curReq, nextReq) if maxCommonCoreType is not None: return maxCommonCoreType.getFormatName().lower() raise InvalidFormatError( 'Track types "%s" and "%s" are not possible to combine. ' % (curVal, nextVal))