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()