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 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 isValidTrack(genome, trackName, fullAccess=False):
if not TrackInfo(genome, trackName).isValid(fullAccess):
return False
for fn in ProcTrackOptions._getDirContents(genome, trackName):
if GenomeInfo.isValidChr(genome, fn) or isBoundingRegionFileName(fn):
return True
return False
def isValidTrack(genome, trackName, fullAccess=False):
if not TrackInfo(genome, trackName).isValid(fullAccess):
return False
for fn in ProcTrackOptions._getDirContents(genome, trackName):
if GenomeInfo.isValidChr(genome,
fn) or isBoundingRegionFileName(fn):
return True
return False
