convert_EDD_from_xls.Rmd

---
title: "convert_EDD_from_xls"
author: "Gavin Lemley"
date: "April 29, 2019"
output: html_document
---

```{r}
# library(dplyr)
library(readxl)
root.dir <- rprojroot::find_root("Chem_raw_processing.Rproj")

# Must create the directories specified in input.path and output.path #
input.path <- file.path(root.dir, "data_input", "convert_edds", "xls")
output.path <- file.path(root.dir, "data_input", "convert_edds", "folders")

```

```{r}

# Initialize loop objects and variables 
file_list <- list.files(path = input.path)
nfile_list = length(file_list)
RSfile_list <- list()
RSfile_list.sample <- list()
i=1

message(paste0(nfile_list, " files present:\n"))

# Loop through each file (folder) present in file_list
for (i in 1:nfile_list){
  print(file_list[i])
  sdg.num <- substr(file_list[i], 1, nchar(file_list[i])-4)
  folder.path <- paste0(output.path,"/",sdg.num,"_conv")
  dir.create(folder.path)
  input.i <- paste0(input.path, "/", file_list[i])
  # output.i <- file.path(root.dir, "data_output")

  temp_sample <- read_xls(input.i, sheet = "Sample_v3", col_names = FALSE)
  
  ##### mutate date format, check if NAs and missing columns are an issue
  
  
  temp_result <- read_xls(input.i, sheet = "TestResultQC_v3", col_names = FALSE)
  temp_batch <- read_xls(input.i, sheet = "Batch_v3", col_names = FALSE)

  write.table(temp_sample, file = paste0(folder.path,"/Sample_v3.txt"), col.names = FALSE, sep = ",", row.names = FALSE)
  write.table(temp_result, file = paste0(folder.path,"/TestResultQC_v3.txt"), col.names = FALSE, sep = ",", row.names = FALSE)
  write.table(temp_batch, file = paste0(folder.path,"/Batch_v3.txt"), col.names = FALSE, sep = ",", row.names = FALSE)
  
}

```