--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_rank_names_to_phyloseq.R	Tue Jan 07 17:58:14 2025 +0000
@@ -0,0 +1,71 @@
+#!/usr/bin/env Rscript
+
+suppressPackageStartupMessages(library("optparse"))
+suppressPackageStartupMessages(library("phyloseq"))
+suppressPackageStartupMessages(library("tidyverse"))
+
+# Option parsing
+option_list <- list(
+    make_option(c("--input"),
+        action = "store", dest = "input",
+        help = "Input file containing a phyloseq object"
+    ),
+    make_option(c("--output"),
+        action = "store", dest = "output",
+        help = "Output file for the updated phyloseq object"
+    ),
+    make_option(c("--ranks"),
+        action = "store", dest = "ranks",
+        help = "Comma-separated list of taxonomy ranks (default: Kingdom,Phylum,Class,Order,Family,Genus,Species)"
+    )
+)
+
+parser <- OptionParser(usage = "%prog [options] file", option_list = option_list)
+args <- parse_args(parser, positional_arguments = TRUE)
+opt <- args$options
+
+cat("Input file: ", opt$input, "\n")
+cat("Output file: ", opt$output, "\n")
+cat("Ranks provided: ", opt$ranks, "\n")
+
+if (is.null(opt$ranks)) {
+    opt$ranks <- "Kingdom,Phylum,Class,Order,Family,Genus,Species"
+}
+
+# Parse rank names
+rank_names <- unlist(strsplit(opt$ranks, ","))
+
+# Load phyloseq object
+physeq <- readRDS(opt$input)
+
+# Check if physeq object is loaded successfully
+if (is.null(physeq)) {
+    stop("Error: Failed to load the Phyloseq object. Check the input file.")
+}
+
+cat("Phyloseq object successfully loaded.\n")
+cat("Class of loaded object: ", class(physeq), "\n")
+
+# Check the current tax_table
+cat("Current tax_table:\n")
+print(tax_table(physeq))
+
+
+# Strict check for taxonomy table and provided ranks
+if (ncol(tax_table(physeq)) != length(rank_names)) {
+    stop(
+        "Error: Number of columns in tax_table does not match the number of provided ranks. ",
+        "Please ensure the taxonomy table matches the ranks exactly."
+    )
+}
+
+# Set column names to the provided ranks
+colnames(tax_table(physeq)) <- rank_names
+
+# Confirm the changes
+cat("Updated tax_table:\n")
+print(tax_table(physeq))
+
+# Save the updated phyloseq object
+saveRDS(physeq, file = opt$output, compress = TRUE)
+cat("Updated Phyloseq object saved to: ", opt$output, "\n")