def __new__(cls, trackName):
if len(trackName) == 0 or trackName is None:
return None
else:
if ExternalTrackManager.isVirtualTrack(trackName):
return VirtualMinimalPlainTrack.__new__(VirtualMinimalPlainTrack)
else:
return object.__new__(cls)
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 _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 _getBoundingRegionShelve(self, trackName):
if trackName in [None, []] or ExternalTrackManager.isVirtualTrack(trackName):
brShelve = None
else:
brShelve = BoundingRegionShelve(self.genome, trackName, allowOverlaps=False)
if not brShelve.fileExists():
raise BoundingRegionsNotAvailableError('Bounding regions not available for track: ' + \
prettyPrintTrackName(trackName))
return brShelve
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 _allGESources(self, trackName):
return [ExternalTrackManager.getGESource(self._fullFn, self._fileSuffix, \
self._extTrackName, self._genome, printWarnings=True)]
def _allGESources(self, trackName):
return [ExternalTrackManager.getGESource(self._fullFn, self._fileSuffix, \
self._extTrackName, self._genome, printWarnings=True)]
