def process(self):
geSource = self._geSourceManager.getGESource()
genome = geSource.genome
collector = PreProcMetaDataCollector(genome, self._trackName)
from gold.origdata.PreProcessTracksJob import PreProcessTracksJob
collector.updateMetaDataForFinalization(geSource.getFileSuffix(), geSource.getPrefixList(),
geSource.getValDataType(), geSource.getValDim(),
geSource.getEdgeWeightDataType(), geSource.getEdgeWeightDim(),
geSource.hasUndirectedEdges(), geSource.getVersion(),
PreProcessTracksJob.VERSION, PreProcessUtils.constructId(geSource),
self._geSourceManager.getNumElements(),
self._geSourceManager.getBoundingRegionTuples(),
self._geSourceManager.getValCategories(),
self._geSourceManager.getEdgeWeightCategories(),
self._allowOverlaps)
if self._geSourceManager.getNumElements() > 0:
if self._mode == 'Real':
output = OutputManager(genome, self._trackName, self._allowOverlaps, self._geSourceManager)
writeFunc = output.writeRawSlice if geSource.isSliceSource() else output.writeElement
for ge in geSource:
writeFunc(ge)
output.close()
else:
for ge in geSource:
pass
if self._mode in ['UpdateMeta', 'Real']:
self._dirty = True
collector.flagChrsAsPreProcessed(self._allowOverlaps, self._geSourceManager.getAllChrs())
def _createPreProcFiles(self):
geSource = self._geSourceManager.getGESource()
genome = geSource.genome
collector = PreProcMetaDataCollector(genome, self._trackName)
collector.updateMetaDataForFinalization(geSource.getFileSuffix(), geSource.getPrefixList(), \
geSource.getValDataType(), geSource.getValDim(), \
geSource.getEdgeWeightDataType(), geSource.getEdgeWeightDim(), \
geSource.hasUndirectedEdges(),
geSource.getVersion(), PreProcessUtils.constructId(geSource), \
self._geSourceManager.getNumElements(), \
self._geSourceManager.getBoundingRegionTuples(), \
self._geSourceManager.getValCategories(), \
self._geSourceManager.getEdgeWeightCategories(), \
self._allowOverlaps)
if self._geSourceManager.getNumElements() == 0:
return
if self._mode != 'Real':
for ge in geSource:
pass
return
output = OutputManager(genome, self._trackName, self._allowOverlaps,
self._geSourceManager)
writeFunc = output.writeRawSlice if geSource.isSliceSource(
) else output.writeElement
for ge in geSource:
writeFunc(ge)
collector.flagChrsAsPreProcessed(self._allowOverlaps,
self._geSourceManager.getAllChrs())
output.close()