data/external_labels/byrnes/extract_labels.R

suppressMessages(library(SeuratObject))
args <- commandArgs(trailingOnly=TRUE)
fn <- args[1]
out <- args[2]

env <- new.env()
loaded <- load(fn, envir=env)
obj <- get(loaded[1], envir=env)
cat("Class:", class(obj)[1], "\n")

# For older Seurat v2 objects, try both @meta.data and metadata slot
md <- tryCatch(slot(obj, "meta.data"), error=function(e) NULL)
if (is.null(md)) {
  # Try Seurat v2 old class (with meta.data field)
  slots <- slotNames(obj)
  cat("Slots:", paste(slots, collapse=","), "\n")
}
if (!is.null(md)) {
  cat("meta.data dim:", nrow(md), "x", ncol(md), "\n")
  cat("meta.data cols:", paste(colnames(md), collapse=", "), "\n")
  write.csv(cbind(cell=rownames(md), md), out, row.names=FALSE)
  cat("wrote", out, "with", nrow(md), "rows\n")
}