Bugfix to handling of nimble append when there are zero rows (#39)

* Bugfix to handling of nimble append when there are zero rows
bimberlabinternal · Jan 10, 2024 · 3c6f4ff · 3c6f4ff
1 parent 590c1aa
commit 3c6f4ff
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diff --git a/R/NimbleAppend.R b/R/NimbleAppend.R
@@ -34,6 +34,11 @@ AppendNimbleCounts <- function(seuratObject, nimbleFile, targetAssayName, dropAm
     }
   })
 
+  # Indicates no data in TSV
+  if (all(is.null(df))){
+    return(seuratObject)
+  }
+
   if (sum(df$V1 == "") > 0) {
     stop("The nimble data contains blank feature names. This should not occur.")
   }

diff --git a/tests/testthat/test-nimbleappend.R b/tests/testthat/test-nimbleappend.R
@@ -13,6 +13,15 @@ test_that("Nimble Append deletes blank feature names when appending", {
   expect_equal(unique(seuratObj@assays$Nimble@meta.features$FeatureSource), c('Nimble'))
 })
 
+test_that("Nimble Append works with empty input", {
+  seuratObj <- Seurat::UpdateSeuratObject(readRDS("../testdata/nimbleTest.rds"))
+  fn <- tempfile(fileext = '.txt')
+  file.create(fn)
+  seuratObj <- AppendNimbleCounts(seuratObj, fn, targetAssayName = 'Nimble')
+  unlink(fn)
+  expect_false('Nimble' %in% names(seuratObj@assays))
+})
+
 test_that("Nimble Append deletes all barcodes not in Seurat when appending", {
   seuratObj <- Seurat::UpdateSeuratObject(readRDS("../testdata/nimbleTest.rds"))
   nimbleExclusiveBarcodes <- c("12345_CCAGCGAAGTCCGTAT", "12345_CCAGCGAAGTCCGTAC")