class OutputDirectory(object):
def __init__(self, path, prefixList, fileArraySize, chrSize, valDataType='float64', valDim=1, \
weightDataType='float64', weightDim=1, maxNumEdges=0, maxStrLens={}, elementsAreSorted=False):
self._files = OrderedDict()
if not os.path.exists(path):
os.makedirs(path)
for prefix in prefixList:
self._files[prefix] = OutputFile(path, prefix, fileArraySize, valDataType, valDim, weightDataType, weightDim, maxNumEdges, maxStrLens)
if 'start' in self._files or 'end' in self._files:
self._indexFiles = OutputIndexFilePair(path, chrSize, self._files.get('start'), self._files.get('end'))
else:
self._indexFiles = None
self._elementsAreSorted = elementsAreSorted
def writeElement(self, genomeElement):
for f in self._files.values():
f.writeElement(genomeElement)
def writeRawSlice(self, genomeElement):
for f in self._files.values():
f.writeRawSlice(genomeElement)
def _sortFiles(self):
startFile = self._files.get('start')
endFile = self._files.get('end')
if startFile and endFile:
sortOrder = np.lexsort((endFile.getContents(), startFile.getContents()))
startFile.sort(sortOrder)
endFile.sort(sortOrder)
elif startFile:
sortOrder = startFile.sort()
elif endFile:
sortOrder = endFile.sort()
else:
sortOrder = None
if sortOrder is not None:
for prefix in self._files.keys():
if prefix not in ['start', 'end']:
self._files[prefix].sort(sortOrder)
def close(self):
if not self._elementsAreSorted:
self._sortFiles()
if self._indexFiles:
self._indexFiles.writeIndexes()
self._indexFiles.close()
for f in self._files.values():
f.close()
def __init__(self, path, prefixList, fileArraySize, chrSize, valDataType='float64', valDim=1, \
weightDataType='float64', weightDim=1, maxNumEdges=0, maxStrLens={}, elementsAreSorted=False):
self._files = OrderedDict()
if not os.path.exists(path):
os.makedirs(path)
for prefix in prefixList:
self._files[prefix] = OutputFile(path, prefix, fileArraySize, valDataType, valDim, weightDataType, weightDim, maxNumEdges, maxStrLens)
if 'start' in self._files or 'end' in self._files:
self._indexFiles = OutputIndexFilePair(path, chrSize, self._files.get('start'), self._files.get('end'))
else:
self._indexFiles = None
self._elementsAreSorted = elementsAreSorted
