def _getTrackView(self, region):
from gold.util.RandomUtil import random # To initialize random generators if not done previously
#if self._cachedTV is None:
rawData = RawDataStat(region, self._origTrack, self._trackFormatReq)
origTV = rawData.getResult()
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(), region)
starts, ends, vals, strands, ids, edges, weights, extras = \
self._undoTrackViewChanges(starts, ends, vals, strands, ids, edges, weights, extras, origTV)
from gold.util.CommonFunctions import getClassName
self._cachedTV = TrackView(origTV.genomeAnchor, starts, ends, 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 getTrackView(self, region):
assert self._origRegion == region
allChrArmRegs = GenomeInfo.getContainingChrArms(region)
if len(allChrArmRegs) != 1:
raise CentromerError
chrArm = allChrArmRegs[0]
buffer = self._getIndepencyBufferSize(region)
sourceRegs = chrArm.exclude( copy(region).extend(-buffer).extend(buffer) )
assert len(sourceRegs) in [1,2]
if not any(len(sourceReg) >= self.MIN_SOURCE_TO_SAMPLE_SIZE_RATIO * len(region) for sourceReg in sourceRegs):
raise TooLargeBinError('Source region lengths of ' + str([len(x) for x in sourceRegs]) +
' are too small compared to region length of ' + str(len(region)) +
' according to MIN_SOURCE_TO_SAMPLE_SIZE_RATIO: ' + str(self.MIN_SOURCE_TO_SAMPLE_SIZE_RATIO))
if len(sourceRegs) == 1:
sourceReg = sourceRegs[0]
else:
firstSourceProportion = (len(sourceRegs[0])-len(region)) / sum(len(sourceRegs[i])-len(region) for i in range(2))
sourceReg = sourceRegs[0] if random.random() < firstSourceProportion else sourceRegs[1]
randOffset = random.randint( 0, len(sourceReg) - len(region) )
start = sourceReg.start + randOffset
end = start + len(region)
randRegion = GenomeRegion(region.genome, region.chr, start, end)
rawData = RawDataStat(randRegion, self._origTrack, self._trackFormatReq)
tv = rawData.getResult()
assert region != tv.genomeAnchor
return tv
def getTrackView(self, region):
#print 'get tv for reg: ',region
#print str(type(self._origRegion)) + " and " + str(type(region))
assert (not isIter(self._origRegion) and self._origRegion == region) or (isIter(self._origRegion) and region in self._origRegion)
#if self._cachedTV is None:
rawData = RawDataStat(region, self._origTrack, self._trackFormatReq)
origTV = rawData.getResult()
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 gold.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 getTrackView(self, region):
# To make sure that the origTrack is only read once across randomizations
rawData = RawDataStat(region, self._origTrack, NeutralTrackFormatReq())
origTv = rawData.getResult()
if not self._trackRandomizer.supportsTrackFormat(origTv.trackFormat):
raise NotSupportedError(
'The original track "{}" has format "{}", '
'which is not supported by "{}".'.format(
prettyPrintTrackName(self.trackName),
str(origTv.trackFormat),
self._trackRandomizer.getDescription()))
if not self._trackRandomizer.supportsOverlapMode(origTv.allowOverlaps):
raise NotSupportedError(
'The original track "{}" has "allowOverlaps={}", '
'which is not supported by "{}".'.format(
prettyPrintTrackName(self.trackName), origTv.allowOverlaps,
self._trackRandomizer.getDescription()))
assert origTv.borderHandling == 'crop'
return origTv