def testShelveLocking(self):
self._setUpShelve()
BoundingRegionShelve('TestGenome', ['testBoundingRegionShelve'],
allowOverlaps=False)
self._commonStoreBoundingRegions(sparse=True)
BoundingRegionShelve('TestGenome', ['testBoundingRegionShelve'],
allowOverlaps=False)
def getTrackData(self,
trackName,
genome,
chr,
allowOverlaps,
forceChrFolders=False):
trackData = TrackData()
brShelve = BoundingRegionShelve(genome, trackName, allowOverlaps)
if not forceChrFolders and brShelve.fileExists():
chr = None
dir = createDirPath(trackName, genome, chr, allowOverlaps)
for fn in os.listdir(dir):
fullFn = dir + os.sep + fn
if fn[0] == '.' or os.path.isdir(fullFn):
continue
if isBoundingRegionFileName(fn):
if fullFn not in self._fileDict:
self._fileDict[fullFn] = brShelve
trackData.boundingRegionShelve = self._fileDict[fullFn]
continue
prefix, elementDim, dtypeDim, dtype = parseMemmapFileFn(fn)
assert prefix not in trackData
trackData[prefix] = self._getFile(chr, dir, fullFn, elementDim,
dtype, dtypeDim)
return trackData
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 __init__(self, genome, trackName, allowOverlaps=False, *args, **kwArgs):
from gtrackcore.track.memmap.BoundingRegionShelve import BoundingRegionShelve
brShelve = BoundingRegionShelve(genome, trackName, allowOverlaps)
if brShelve.fileExists():
boundingRegions = list(brShelve.getAllBoundingRegions())
else:
boundingRegions = GenomeInfo.getStdChrRegionList(genome)
TrackGenomeElementSource.__init__(self, genome=genome, trackName=trackName, \
boundingRegions=boundingRegions, globalCoords=True, \
allowOverlaps=allowOverlaps, printWarnings=True)
def _setUpShelve(self):
self._brShelve = BoundingRegionShelve('TestGenome',
['testBoundingRegionShelve'],
allowOverlaps=False)
