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 _compute(self):
rawData = self._children[0].getResult()
ends = rawData.endsAsNumpyArray()
starts = rawData.startsAsNumpyArray()
catSequence = rawData.valsAsNumpyArray()
if catSequence is None:
raise IncompatibleTracksError()
catSet = numpy.unique(catSequence)
res = {}
for cat in catSet:
filter = (catSequence == cat)
if rawData.trackFormat.reprIsDense():
res[cat] = filter.sum()
else:
#print 'BpCoverage..: ',ends, starts, catSequence, catSet, type(catSequence), filter
#res[cat] = ends[filter].sum() - starts[filter].sum()
catStarts = starts[filter]
catEnds = ends[filter]
totCoverage = catEnds.sum() - catStarts.sum()
runningMaxEnds = numpy.maximum.accumulate(catEnds)
tempArray1 = runningMaxEnds[:-1] - catStarts[1:]
tempArray2 = runningMaxEnds[:-1] - catEnds[1:]
totOverlap = tempArray1[tempArray1 > 0].sum() - tempArray2[
tempArray2 > 0].sum()
res[cat] = totCoverage - totOverlap
return res
def getTrackView(self, region):
if self.formatConverters is None:
self.formatConverters = getFormatConverters(
self._tv.trackFormat, self._trackFormatReq)
if self.formatConverters == []:
raise IncompatibleTracksError('Track with format: '\
+ str(self._tv.trackFormat) +
('(' + self._tv.trackFormat._val + ')' if self._tv.trackFormat._val else '') + \
' does not satisfy ' + str(self._trackFormatReq))
if not self.formatConverters[0].canHandle(self._tv.trackFormat,
self._trackFormatReq):
raise IncompatibleTracksError(getClassName(self.formatConverters[0]) +\
' does not support conversion from ' + str(self._tv.trackFormat) + \
' to ' + str(self._trackFormatReq))
return self.formatConverters[0].convert(self._tv[region.start - self._tv.genomeAnchor.start : \
region.end - self._tv.genomeAnchor.start])
def _getRawTrackView(self, region, borderHandling, allowOverlaps):
assert len(region) == 1
from collections import OrderedDict
from gold.track.CommonMemmapFunctions import findEmptyVal
from gold.track.TrackView import TrackView
import numpy as np
geSource = ExternalTrackManager.getGESourceFromGalaxyOrVirtualTN(self.trackName, region.genome)
prefixList = geSource.getPrefixList()
valDataType = geSource.getValDataType()
valDim = geSource.getValDim()
weightDataType = geSource.getEdgeWeightDataType()
weightDim = geSource.getEdgeWeightDim()
startList, endList, valList, strandList, idList, edgesList, weightsList = [None]*7
extraLists=OrderedDict()
tf = TrackFormat.createInstanceFromPrefixList(prefixList, valDataType, valDim, \
weightDataType, weightDim)
if allowOverlaps and (tf.isDense() or geSource.hasNoOverlappingElements()):
raise IncompatibleTracksError(prettyPrintTrackName(self.trackName) + ' with format: '\
+ str(tf) + ' does not satisfy ' + str(self._trackFormatReq))
denseAndInterval = tf.isDense() and tf.isInterval()
numEls = 2 if denseAndInterval else 1
if valDataType == 'S':
valDataType = 'S2'
if weightDataType == 'S':
weightDataType = 'S2'
for prefix in prefixList:
if prefix == 'start':
startList = np.array([-1], dtype='int32')
elif prefix == 'end':
if denseAndInterval:
endList = np.array([0, 1], dtype='int32')
else:
endList = np.array([0], dtype='int32')
elif prefix == 'val':
valList = np.array([findEmptyVal(valDataType)] * valDim * numEls, \
dtype=valDataType).reshape((numEls, valDim) if valDim > 1 else numEls)
elif prefix == 'strand':
strandList = np.array([1] * numEls, dtype='int8')
elif prefix == 'id':
idList = np.array([''] * numEls, dtype='S1')
elif prefix == 'edges':
edgesList = np.array([['']] * numEls, dtype='S1')
elif prefix == 'weights':
weightsList = np.array([[[findEmptyVal(weightDataType)]]] * weightDim * numEls, \
dtype=weightDataType).reshape((numEls, 1, weightDim) if weightDim > 1 else (numEls, 1))
else:
extraLists[prefix] = np.array([''] * numEls, dtype='S1')
return TrackView(region, startList, endList, valList, strandList, idList, edgesList, weightsList, borderHandling, allowOverlaps, extraLists)
def _checkTrackFormat(self, origTV):
# Commented out, as segments are not currently supported at all (end list is never returned)
#
#if origTV.trackFormat.isDense():
# raise IncompatibleTracksError()
#
#if origTV.trackFormat.isInterval():
# if not IS_EXPERIMENTAL_INSTALLATION:
# raise IncompatibleTracksError
if origTV.trackFormat.isDense() or origTV.trackFormat.isInterval():
raise IncompatibleTracksError()
def _compute(self):
rawData = self._children[0].getResult()
starts = rawData.startsAsNumpyArray()
catSequence = rawData.valsAsNumpyArray()
if catSequence is None:
raise IncompatibleTracksError()
catSet = numpy.unique(catSequence)
res = OrderedDict()
for cat in catSet:
filter = (catSequence == cat)
res[cat] = len(numpy.unique(starts[filter]))
return res
def _validateAllTracksRead(self):
if not self.hasResult():
raise ShouldNotOccurError("At this stage, statistic should either have result, "
"or exception should have been raised")
tracks = self.getAllTracks()
trackUniqueKeys = [Track(tr.trackName).getUniqueKey(self.getGenome()) for tr in tracks]
for trackIndex, restTrackIndexes in allElementsVersusRest(xrange(len(trackUniqueKeys))):
track = tracks[trackIndex]
if track is not None and not track.hasBeenFlaggedAsRead():
uniqueKeyForRestTracks = \
set(trackUniqueKeys[i] for i in restTrackIndexes)
# If several tracks are the same, memory memoization will only result
# in one RawDataStat being created, for one Track object. This is a
# wanted optimization. In other cases, something is probably wrong if
# a track has not been touched. However, this rule may be revisited
# when track structure functionality is implemented.
if trackUniqueKeys[trackIndex] not in uniqueKeyForRestTracks:
raise IncompatibleTracksError(
'Track ' + prettyPrintTrackName(track.trackName) +
' was created, but not touched by statistic')
def _determineStatClass(self):
assert( hasattr(self, '_track') )
assert( hasattr(self, '_track2') )
dummyGESource = MinimalBinSource(self._genome)
if len(self._statClassList)==0:
#logging.getLogger(HB_LOGGER).warning('Stat class list is empty, for analysisDef: ' + self._analysisLine)
if self._reversed:
logMessage('Stat class list is empty, for analysisDef: ' + self._analysisLine, level = logging.WARNING)
if DebugConfig.PASS_ON_VALIDSTAT_EXCEPTIONS:
raise ShouldNotOccurError('Stat class list is empty. Analysisdef: '+self._analysisLine)
for statClass in self._statClassList:
if DebugConfig.VERBOSE:
logMessage(statClass.__name__ + ': Trying (' + self.getDefAfterChoices() + ')')
# print statClass.__name__ + ': Trying (' + self.getDefAfterChoices() + ')'
#for reversed, trackA, trackB in [(False, self._track, self._track2), (True, self._track2, self._track) ]:
trackA, trackB = self._track, self._track2
if trackA is None:
continue
try:
# The hackiest of all hacks!
# TODO: reimplement together with TrackStructure
job = StatJob(dummyGESource, trackA, trackB, statClass, minimal=True,
**self.getChoices(filterByActivation=True))
stat = job._getSingleResult(dummyGESource[0])[-1]
tracks = stat._tracks if hasattr(stat, '_tracks') else [trackA, trackB]
trackUniqueKeys = [Track(tr.trackName).getUniqueKey(self._genome) for tr in tracks
if tr is not None]
StatJob(dummyGESource, trackA, trackB, statClass, minimal=True,
**self.getChoices(filterByActivation=True)).run(False)
#In order not to mess up integration tests
initSeed()
for trackIndex, restTrackIndexes in allElementsVersusRest(xrange(len(tracks))):
track = tracks[trackIndex]
if track is not None and track.formatConverters is None:
uniqueKeyForRestTracks = \
set(trackUniqueKeys[i] for i in restTrackIndexes)
# If several tracks are the same, memory memoization will only result
# in one RawDataStat being created, for one Track object. This is a
# wanted optimization. In other cases, something is probably wrong if
# a track has not been touched. However, this rule may be revisited
# when track structure functionality is implemented.
if trackUniqueKeys[trackIndex] not in uniqueKeyForRestTracks:
raise IncompatibleTracksError(
'Track ' + prettyPrintTrackName(track.trackName) +
' was created, but not touched by statistic')
except IncompatibleTracksError, e:
if DebugConfig.VERBOSE:
logException(e, level=logging.DEBUG,
message='(Warning: error in _determineStatClass for stat: %s)' % statClass.__name__)
if DebugConfig.PASS_ON_VALIDSTAT_EXCEPTIONS:
raise
except (AssertionError, IncompatibleAssumptionsError, IdenticalTrackNamesError), e:
if DebugConfig.VERBOSE:
logException(e, level=logging.DEBUG,
message='(Warning: error in _determineStatClass for stat: %s)' % statClass.__name__)
if DebugConfig.PASS_ON_VALIDSTAT_EXCEPTIONS:
raise
def addFormatReq(self, requestedTrackFormat):
if not self._ignoreTrackFormat and requestedTrackFormat != None and not requestedTrackFormat.isCompatibleWith(
self._tv.trackFormat):
raise IncompatibleTracksError(
str(requestedTrackFormat) + ' not compatible with ' +
str(self._tv.trackFormat))
def _checkTrackFormat(self, origTV):
if origTV.trackFormat.isDense():
raise IncompatibleTracksError()
def supportsTrackFormat(cls, origTrackFormat):
if origTrackFormat.trackFormat.isDense():
raise IncompatibleTracksError()
def _checkTrackFormat(self, origTV):
if not origTV.trackFormat.isValued():
raise IncompatibleTracksError(str(origTV.trackFormat))