server-scripts/qhtcp-workflow/apps/r/CompileGTF.R

#!/usr/bin/env Rscript

# Load the openxlsx package
library(openxlsx)

args <- commandArgs(TRUE)

outDir <- args[1]

# Function to combine CSV and TXT files into a workbook with named sheets
combineFilesToWorkbook <- function(file_list, output_file) {
  # Create a new workbook
  wb <- createWorkbook()
  
  # Loop through the file list
  for (i in seq_along(file_list)) {
    file <- file_list[i]
    
    # Extract the sheet name from the file name based on the extension
    ext <- tools::file_ext(file)
    sheet_name <- tools::file_path_sans_ext(basename(file))
    
    # Read the data based on the file extension
    if (ext %in% c("csv", "txt")) {
      if (ext == "csv") {
        data <- read.csv(file)
      } else if (ext == "txt") {
        data <- readLines(file)
      }
      
      # Create a new sheet in the workbook with the extracted sheet name
      addWorksheet(wb, sheetName = sheet_name)
      
      # Write the data to the sheet
      writeData(wb, sheet = sheet_name, x = data)
    }
  }
  
  # Save the workbook as an Excel file
  saveWorkbook(wb, output_file)
}

Component <- file.path(outDir, "Component", "ComponentResults.txt")
Function <- file.path(outDir, "Function", "FunctionResults.txt")
Process <- file.path(outDir, "Process", "ProcessResults.txt")

# Specify the list of input files (both CSV and TXT)
file_list <- c(Component, Process, Function)

# Specify the output file name
output_file <- file.path(outDir, "GTFCombined.xlsx")

# Call the function to combine the files into a workbook with named sheets
combineFilesToWorkbook(file_list, output_file)