def __init__(self, trackName): self.trackName = trackName self._trackSource = TrackSource() self._trackViewLoader = TrackViewLoader() self._trackFormatReq = NeutralTrackFormatReq() self.formatConverters = None self._trackId = None
def __init__(self, trackView, ignoreTrackFormat=False): self._tv = trackView self.trackName = ['dummy' + str(SampleTrackWithConverters.trackNo)] self._ignoreTrackFormat = ignoreTrackFormat SampleTrackWithConverters.trackNo += 1 self.formatConverters = None self._trackFormatReq = NeutralTrackFormatReq()
class RandomizedTrack(Track): IS_MEMOIZABLE = False def __new__(cls, *args, **kwArgs): return object.__new__(cls) def __init__(self, origTrack, origRegion, randIndex, **kwArgs ): self._origTrack = origTrack self.trackName = origTrack.trackName + ['Randomized', str(randIndex)] self._origRegion = origRegion self._trackFormatReq = NeutralTrackFormatReq() self._cachedTV = None def _checkTrackFormat(self, origTV): pass def getTrackView(self, region): #print 'get tv for reg: ',region #print str(type(self._origRegion)) + " and " + str(type(region)) if Config.USE_SLOW_DEFENSIVE_ASSERTS: assert (not isIter(self._origRegion) and self._origRegion == region) or \ (isIter(self._origRegion) and region in self._origRegion) #if self._cachedTV is None: self._origTrack.addFormatReq(self._trackFormatReq) origTV = self._origTrack.getTrackView(region) self._checkTrackFormat(origTV) assert(not origTV.allowOverlaps) assert(origTV.borderHandling == 'crop') assert region == origTV.genomeAnchor starts, ends, vals, strands, ids, edges, weights, extras = \ self._createRandomizedNumpyArrays(len(origTV.genomeAnchor), origTV.startsAsNumpyArray(), \ origTV.endsAsNumpyArray(), origTV.valsAsNumpyArray(), \ origTV.strandsAsNumpyArray(), origTV.idsAsNumpyArray(), \ origTV.edgesAsNumpyArray(), origTV.weightsAsNumpyArray(), \ origTV.allExtrasAsDictOfNumpyArrays(), origTV.trackFormat, region) from gtrackcore.util.CommonFunctions import getClassName self._cachedTV = TrackView(origTV.genomeAnchor, \ (starts + origTV.genomeAnchor.start if starts is not None else None), \ (ends + origTV.genomeAnchor.start if ends is not None else None), \ vals, strands, ids, edges, weights, origTV.borderHandling, origTV.allowOverlaps, extraLists=extras) assert self._trackFormatReq.isCompatibleWith(self._cachedTV.trackFormat), 'Incompatible track-format: '\ + str(self._trackFormatReq) + ' VS ' + str(self._cachedTV.trackFormat) return self._cachedTV def _createRandomizedNumpyArrays(self, binLen, starts, ends, vals, strands, ids, edges, weights, extras, origTrackFormat, region): raise AbstractClassError
class Track(object): IS_MEMOIZABLE = True def __new__(cls, trackName): if trackName == [] or trackName is None: return None else: if ExternalTrackManager.isVirtualTrack(trackName): return VirtualMinimalTrack.__new__(VirtualMinimalTrack) else: return object.__new__(cls) def __init__(self, trackName): self.trackName = trackName self._trackSource = TrackSource() self._trackViewLoader = TrackViewLoader() self._trackFormatReq = NeutralTrackFormatReq() self.formatConverters = None self._trackId = None def _getRawTrackView(self, region, borderHandling, allowOverlaps): trackData = self._trackSource.getTrackData(self.trackName, region.genome, region.chr, allowOverlaps) return self._trackViewLoader.loadTrackView(trackData, region, borderHandling, allowOverlaps, self.trackName) def getTrackView(self, region): allowOverlaps = self._trackFormatReq.allowOverlaps() borderHandling = self._trackFormatReq.borderHandling() assert (allowOverlaps is not None) assert (borderHandling is not None) origTrackView = self._getRawTrackView(region, borderHandling, allowOverlaps) if self.formatConverters is None: self.formatConverters = getFormatConverters( origTrackView.trackFormat, self._trackFormatReq) if self.formatConverters == []: raise IncompatibleTracksError(prettyPrintTrackName(self.trackName) + ' with format: '\ + str(origTrackView.trackFormat) + ('(' + origTrackView.trackFormat._val + ')' if origTrackView.trackFormat._val else '') + \ ' does not satisfy ' + str(self._trackFormatReq)) if not self.formatConverters[0].canHandle(origTrackView.trackFormat, self._trackFormatReq): raise IncompatibleTracksError(getClassName(self.formatConverters[0]) +\ ' does not support conversion from ' + str(origTrackView.trackFormat) + \ ' to ' + str(self._trackFormatReq)) return self.formatConverters[0].convert(origTrackView) def addFormatReq(self, requestedTrackFormat): prevFormatReq = self._trackFormatReq self._trackFormatReq = TrackFormatReq.merge(self._trackFormatReq, requestedTrackFormat) if self._trackFormatReq is None: raise IncompatibleTracksError(str(prevFormatReq ) + \ ' is incompatible with additional ' + str(requestedTrackFormat)) def setFormatConverter(self, converterClassName): assert (self.formatConverters is None) if converterClassName is not None: self.formatConverters = [ getFormatConverterByName(converterClassName) ] def getUniqueKey(self, genome): assert self.formatConverters is not None and len( self.formatConverters) == 1, 'FC: ' + str(self.formatConverters) assert( not None in [self._trackFormatReq.allowOverlaps(), \ self._trackFormatReq.borderHandling()] ) if not self._trackId: self._trackId = TrackInfo(genome, self.trackName).id return hash((tuple(self.trackName), self._trackId, getClassName(self.formatConverters[0]), \ self.formatConverters[0].VERSION, self._trackFormatReq.allowOverlaps(), \ self._trackFormatReq.borderHandling()))
def __init__(self, origTrack, origRegion, randIndex, **kwArgs ): self._origTrack = origTrack self.trackName = origTrack.trackName + ['Randomized', str(randIndex)] self._origRegion = origRegion self._trackFormatReq = NeutralTrackFormatReq() self._cachedTV = None
class Track(object): IS_MEMOIZABLE = True def __new__(cls, trackName): if trackName == [] or trackName is None: return None else: if ExternalTrackManager.isVirtualTrack(trackName): return VirtualMinimalTrack.__new__(VirtualMinimalTrack) else: return object.__new__(cls) def __init__(self, trackName): self.trackName = trackName self._trackSource = TrackSource() self._trackViewLoader = TrackViewLoader() self._trackFormatReq = NeutralTrackFormatReq() self.formatConverters = None self._trackId = None def _getRawTrackView(self, region, borderHandling, allowOverlaps): trackData = self._trackSource.getTrackData(self.trackName, region.genome, region.chr, allowOverlaps) return self._trackViewLoader.loadTrackView(trackData, region, borderHandling, allowOverlaps, self.trackName) def getTrackView(self, region): allowOverlaps = self._trackFormatReq.allowOverlaps() borderHandling = self._trackFormatReq.borderHandling() assert(allowOverlaps is not None) assert(borderHandling is not None) origTrackView = self._getRawTrackView(region, borderHandling, allowOverlaps) if self.formatConverters is None: self.formatConverters = getFormatConverters(origTrackView.trackFormat, self._trackFormatReq) if self.formatConverters == []: raise IncompatibleTracksError(prettyPrintTrackName(self.trackName) + ' with format: '\ + str(origTrackView.trackFormat) + ('(' + origTrackView.trackFormat._val + ')' if origTrackView.trackFormat._val else '') + \ ' does not satisfy ' + str(self._trackFormatReq)) if not self.formatConverters[0].canHandle(origTrackView.trackFormat, self._trackFormatReq): raise IncompatibleTracksError(getClassName(self.formatConverters[0]) +\ ' does not support conversion from ' + str(origTrackView.trackFormat) + \ ' to ' + str(self._trackFormatReq)) return self.formatConverters[0].convert(origTrackView) def addFormatReq(self, requestedTrackFormat): prevFormatReq = self._trackFormatReq self._trackFormatReq = TrackFormatReq.merge(self._trackFormatReq, requestedTrackFormat) if self._trackFormatReq is None: raise IncompatibleTracksError(str(prevFormatReq ) + \ ' is incompatible with additional ' + str(requestedTrackFormat)) def setFormatConverter(self, converterClassName): assert( self.formatConverters is None ) if converterClassName is not None: self.formatConverters = [getFormatConverterByName(converterClassName)] def getUniqueKey(self, genome): assert self.formatConverters is not None and len(self.formatConverters) == 1, 'FC: '+str(self.formatConverters) assert( not None in [self._trackFormatReq.allowOverlaps(), \ self._trackFormatReq.borderHandling()] ) if not self._trackId: self._trackId = TrackInfo(genome, self.trackName).id return hash((tuple(self.trackName), self._trackId, getClassName(self.formatConverters[0]), \ self.formatConverters[0].VERSION, self._trackFormatReq.allowOverlaps(), \ self._trackFormatReq.borderHandling()))