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 _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 _allGESources(self, trackName):
return [ExternalTrackManager.getGESource(self._fullFn, self._fileSuffix, \
self._extTrackName, self._genome, printWarnings=True)]
def _getRawTrackView(self, region, borderHandling, allowOverlaps):
assert len(region) == 1
from collections import OrderedDict
from gtrackcore_memmap.track.memmap.CommonMemmapFunctions import findEmptyVal
from gtrackcore_memmap.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,
)
