Auto-add missing columns to PredictTcellActivation

bbimber · bbimber · commit 30eda781cc81 · 2026-01-07T06:36:15.000-08:00
(cherry picked from commit b506b87)
diff --git a/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R b/singlecell/resources/chunks/IdentifyAndStoreActiveClonotypes.R
@@ -11,6 +11,11 @@ for (datasetId in names(seuratObjects)) {
   printName(datasetId)
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
+  if (! 'TRB_Segments' %in% names(seuratObj@meta.data)) {
+    print('Re-running AppendTcr to add segment columns')
+    seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = TRUE)
+  }
+
   Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRA', storeStimLevelData = FALSE)
   Rdiscvr::IdentifyAndStoreActiveClonotypes(seuratObj, chain = 'TRB')
 
diff --git a/singlecell/resources/chunks/PredictTcellActivation.R b/singlecell/resources/chunks/PredictTcellActivation.R
@@ -10,6 +10,11 @@ for (datasetId in names(seuratObjects)) {
     }
   }
 
+  if (! 'TRB_Segments' %in% names(seuratObj@meta.data)) {
+    print('Re-running AppendTcr to add segment columns')
+    seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = TRUE)
+  }
+
   seuratObj <- RIRA::PredictTcellActivation(seuratObj)
 
   saveData(seuratObj, datasetId)

Original file line number	Diff line number	Diff line change
`@@ -10,6 +10,11 @@ for (datasetId in names(seuratObjects)) {`
`10`	`10`	`}`
`11`	`11`	`}`
`12`	`12`
	`13`	`+ if (! 'TRB_Segments' %in% names(seuratObj@meta.data)) {`
	`14`	`+ print('Re-running AppendTcr to add segment columns')`
	`15`	`+ seuratObj <- Rdiscvr::DownloadAndAppendTcrClonotypes(seuratObj, allowMissing = TRUE)`
	`16`	`+ }`
	`17`	`+`
`13`	`18`	`seuratObj <- RIRA::PredictTcellActivation(seuratObj)`
`14`	`19`
`15`	`20`	`saveData(seuratObj, datasetId)`