Save metadata table from Seurat objects

Author: bbimber

singlecell/resources/chunks/SaveData.R

@@ -4,6 +4,7 @@ for (datasetId in names(newSeuratObjects)) {
 
     fn <- paste0(outputPrefix, '.', datasetId, '.seurat.rds')
     barcodeFile <- paste0(outputPrefix, '.', datasetId, '.cellBarcodes.csv')
+    metaFile <- paste0(outputPrefix, '.', datasetId, '.seurat.meta.txt')
 
     saveRDS(seuratObj, file = fn)
 
@@ -14,7 +15,8 @@ for (datasetId in names(newSeuratObjects)) {
 
     savedFiles <- rbind(savedFiles, data.frame(datasetId = datasetId, datasetName = datasetName, filename = fn, outputFileId = outputFileId))
 
-    # WriteCellBarcodes
+    # Write cell barcodes and metadata:
+    write.table(seuratObj@meta.data, file = metaFile, quote = F, row.names = F, sep = ',', col.names = F)
     write.table(data.frame(CellBarcode = colnames(seuratObj)), file = barcodeFile, quote = F, row.names = F, sep = ',', col.names = F)
 }
 

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -1089,4 +1089,15 @@ public File getCellBarcodesFromSeurat(File seuratObj)
 
         return barcodes;
     }
+
+    public File getMetaTableFromSeurat(File seuratObj)
+    {
+        File barcodes = new File(seuratObj.getParentFile(), seuratObj.getName().replaceAll("seurat.rds", "seurat.meta.txt"));
+        if (!barcodes.exists())
+        {
+            throw new IllegalArgumentException("Unable to find expected metadata file.  This might indicate the seurat object was created with an older version of the pipeline.  Expected: " + barcodes.getPath());
+        }
+
+        return barcodes;
+    }
 }

singlecell/src/org/labkey/singlecell/analysis/AbstractSingleCellHandler.java

@@ -291,6 +291,7 @@ else if (step.createsSeuratObjects())
                     currentFiles = new ArrayList<>(output.getSeuratObjects());
                     _resumer.getFileManager().addIntermediateFiles(currentFiles.stream().map(SingleCellStep.SeuratObjectWrapper::getFile).collect(Collectors.toSet()));
                     _resumer.getFileManager().addIntermediateFiles(currentFiles.stream().map(x -> CellHashingServiceImpl.get().getCellBarcodesFromSeurat(x.getFile())).collect(Collectors.toSet()));
+                    _resumer.getFileManager().addIntermediateFiles(currentFiles.stream().map(x -> CellHashingServiceImpl.get().getMetaTableFromSeurat(x.getFile())).collect(Collectors.toSet()));
                 }
                 else if (step.createsSeuratObjects())
                 {
@@ -316,6 +317,7 @@ else if (step.createsSeuratObjects())
                     ctx.getFileManager().removeIntermediateFile(seurat.getFile());
                     _resumer.getFileManager().removeIntermediateFile(seurat.getFile());
                     _resumer.getFileManager().removeIntermediateFile(CellHashingServiceImpl.get().getCellBarcodesFromSeurat(seurat.getFile()));
+                    _resumer.getFileManager().removeIntermediateFile(CellHashingServiceImpl.get().getMetaTableFromSeurat(seurat.getFile()));
                 }
             }
 
@@ -471,6 +473,7 @@ private List<SingleCellStep.SeuratObjectWrapper> processRawCounts(JobContext ctx
             }
             currentFiles.stream().map(SingleCellStep.SeuratObjectWrapper::getFile).forEach(_resumer.getFileManager()::addIntermediateFile);
             _resumer.getFileManager().addIntermediateFiles(currentFiles.stream().map(x -> CellHashingServiceImpl.get().getCellBarcodesFromSeurat(x.getFile())).collect(Collectors.toSet()));
+            _resumer.getFileManager().addIntermediateFiles(currentFiles.stream().map(x -> CellHashingServiceImpl.get().getMetaTableFromSeurat(x.getFile())).collect(Collectors.toSet()));
 
             _resumer.setStepComplete(ctx.getLogger(), prepareRawCounts, 0, action, output0.getSeuratObjects(), output0.getMarkdownFile(), output0.getHtmlFile());
         }