def __init__(self, trackName):
self.trackName = trackName
self._trackSource = TrackSource()
self._trackViewLoader = TrackViewLoader()
self._trackFormatReq = NeutralTrackFormatReq()
self.formatConverters = None
self._trackId = None
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_memmap.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
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(),
)
)