def merge(genome, trackName, allowOverlaps):
path = createDirPath(trackName, genome, allowOverlaps=allowOverlaps)
collector = PreProcMetaDataCollector(genome, trackName)
chrList = collector.getPreProcessedChrs(allowOverlaps)
if not collector.getTrackFormat().reprIsDense():
chrList = sorted(chrList)
existingChrList = [
chr
for chr in ChrMemmapFolderMerger._existingChrIter(path, chrList)
]
if len(existingChrList) == 0:
raise EmptyGESourceError(
'No data lines has been read from source file (probably because it is empty).'
)
firstChrTrackData = TrackSource().getTrackData(trackName,
genome,
existingChrList[0],
allowOverlaps,
forceChrFolders=True)
arrayList = firstChrTrackData.keys()
for arrayName in arrayList:
mergedArray = firstChrTrackData[arrayName][:]
elementDim, dtypeDim = parseMemmapFileFn(
firstChrTrackData[arrayName].filename)[1:3]
del firstChrTrackData[arrayName]
for chr in existingChrList[1:]:
chrTrackData = TrackSource().getTrackData(trackName,
genome,
chr,
allowOverlaps,
forceChrFolders=True)
mergedArray = ChrMemmapFolderMerger.mergeArrays(
mergedArray, np.array(chrTrackData[arrayName][:]))
elementDimNew, dtypeDimNew = parseMemmapFileFn(
chrTrackData[arrayName].filename)[1:3]
elementDim = max(elementDim, elementDimNew)
dtypeDim = max(dtypeDim, dtypeDimNew)
del chrTrackData[arrayName]
mergedFn = createMemmapFileFn(path, arrayName, elementDim,
dtypeDim, str(mergedArray.dtype))
f = np.memmap(mergedFn,
dtype=mergedArray.dtype,
mode='w+',
shape=mergedArray.shape)
f[:] = mergedArray
f.flush()
del f
del mergedArray
def __init__(self, trackName):
self.trackName = trackName
self._trackSource = TrackSource()
self._trackViewLoader = TrackViewLoader()
self._trackFormatReq = NeutralTrackFormatReq()
self.formatConverters = None
self._trackId = None
def _getTrackData(self):
for br in self._boundingRegions:
chr = br.chr
break
return TrackSource().getTrackData(self._trackName, self._genome, chr, allowOverlaps=self._allowOverlaps)
