fix writeBambuOutpur error when this is no novel transcript in se object

suiyue · suiyue · commit 7315f89361f4 · 2025-02-03T12:48:30.000+08:00
diff --git a/R/readWrite.R b/R/readWrite.R
@@ -249,8 +249,13 @@ writeAnnotationsToGTF <- function(annotation, file, geneIDs = NULL, outputExtend
     }
 
     if(outputNovelOnly){
+        if(all(!rowData(se)$novelTranscript)){
+          print("This is no novel transcript and novelTranscripts.gtf will not be outputed!")
+        }
+      else{
         annotationNovel = annotation[mcols(annotation)$novelTranscript]
         writeToGTF(annotationNovel, paste0(file, "novelTranscripts.gtf"), geneIDs)
+      }
     }
 }
 

Original file line number	Diff line number	Diff line change
`@@ -249,8 +249,13 @@ writeAnnotationsToGTF <- function(annotation, file, geneIDs = NULL, outputExtend`
`249`	`249`	`}`
`250`	`250`
`251`	`251`	`if(outputNovelOnly){`
	`252`	`+ if(all(!rowData(se)$novelTranscript)){`
	`253`	`+ print("This is no novel transcript and novelTranscripts.gtf will not be outputed!")`
	`254`	`+ }`
	`255`	`+ else{`
`252`	`256`	`annotationNovel = annotation[mcols(annotation)$novelTranscript]`
`253`	`257`	`writeToGTF(annotationNovel, paste0(file, "novelTranscripts.gtf"), geneIDs)`
	`258`	`+ }`
`254`	`259`	`}`
`255`	`260`	`}`
`256`	`261`