Prepare to support CalculateTcrRepertoireStats

Author: bbimber

singlecell/resources/chunks/CalculateTcrRepertioreStats.R

@@ -0,0 +1,18 @@
+netRc <- paste0(Sys.getenv('USER_HOME'), '/.netrc')
+if (!file.exists(netRc)) {
+  print(list.files(Sys.getenv('USER_HOME')))
+  stop(paste0('Unable to find file: ', netRc))
+}
+
+invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = netRc))
+Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
+
+for (datasetId in names(seuratObjects)) {
+  printName(datasetId)
+  seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+  seuratObj <- Rdiscvr::CalculateAndStoreTcrRepertioreStats(seuratObj)
+
+  # Cleanup
+  rm(seuratObj)
+  gc()
+}

singlecell/src/org/labkey/singlecell/SingleCellModule.java

@@ -45,6 +45,7 @@
 import org.labkey.singlecell.pipeline.singlecell.ApplyKnownClonotypicData;
 import org.labkey.singlecell.pipeline.singlecell.AvgExpression;
 import org.labkey.singlecell.pipeline.singlecell.CalculateGeneComponentScores;
+import org.labkey.singlecell.pipeline.singlecell.CalculateTcrRepertoireStats;
 import org.labkey.singlecell.pipeline.singlecell.CalculateUCellScores;
 import org.labkey.singlecell.pipeline.singlecell.CellBarcodeFilter;
 import org.labkey.singlecell.pipeline.singlecell.CheckExpectations;
@@ -301,6 +302,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new PerformMhcDimRedux.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunTricycle.Provider());
         SequencePipelineService.get().registerPipelineStep(new ApplyKnownClonotypicData.Provider());
+        SequencePipelineService.get().registerPipelineStep(new CalculateTcrRepertoireStats.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

singlecell/src/org/labkey/singlecell/pipeline/singlecell/CalculateTcrRepertoireStats.java

@@ -0,0 +1,43 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.Arrays;
+
+public class CalculateTcrRepertoireStats extends AbstractRDiscvrStep
+{
+    public CalculateTcrRepertoireStats(PipelineContext ctx, CalculateTcrRepertoireStats.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("CalculateTcrRepertoireStats", "Calculate TCR Repertoire Stats", "CellMembrane/tcrdist3", "This will calculate TCR diversity metrics, and save the results in the database.", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public CalculateTcrRepertoireStats create(PipelineContext ctx)
+        {
+            return new CalculateTcrRepertoireStats(ctx, this);
+        }
+    }
+
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "ts";
+    }
+}