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 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 gtrackcore.track.memmap.CommonMemmapFunctions import findEmptyVal
from gtrackcore.track.core.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):
if origTV.trackFormat.isDense():
raise IncompatibleTracksError()
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 not origTV.trackFormat.isValued():
raise IncompatibleTracksError(str(origTV.trackFormat))