diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 45 |
1 files changed, 20 insertions, 25 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index 283ceef..a6432d7 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -22,40 +22,35 @@ make_option(c("-o", "--output_file"), action="store", default=NULL, type='charac opt <- parse_args(OptionParser(option_list=option_list)) -# check for mandatory args -if(is.null(opt$directory)){ -stop("You need to specify a working temporary directory which should have be base_dir for the input file") -} - NO_OF_CORES = opt$cores SCAN_METHOD = opt$method NO_OF_PERMUTATION = opt$nperm -# get the json file path with pre metadata required to create the cross -# assumption is that the input file should be in the temp working directory +# Step: check for mandatory file paths +# NOTE this is the working dir should be the path for both INPUT and OUTPUT_FILE +# NOTE this is where the cross file is generated -if (is.null(opt$input_file)) { - stop("Argument for the Input metadata file is Missing ", call. = FALSE) -} else { - input_file = opt$input_file +if(is.null(opt$directory) || !(dir.exists(opt$directory))){ +# check if directory exists +stop("The working directory does not exists or is NULL\n") } -if (is.null(opt$output_file)){ -stop("You need to provide an output file to write the ouput data") -} - -# file_path -input_file_path = file.path(opt$directory, input_file) +INPUT_FILE_PATH = file.path(opt$directory, opt$input_file) +OUTPUT_FILE_PATH = file.path(opt$directory , opt$output_file) -if (!(file.exists(input_file_path))) { - stop("The input file you provided does not exists the temp directory") +if (!(file.exists(INPUT_FILE_PATH))) { + stop("The input file", INPUT_FILE_PATH, " you provided does not exists the directory", opt$directory, "\n") } else { - cat("The input file for the metadata is >>>>>", input_file_path, "\n") - json_data = fromJSON(file = input_file_path) + cat("Input file exists Reading the input file .... ", INPUT_FILE_PATH, "\n") + json_data = fromJSON(file = INPUT_FILE_PATH) +} +if (!(file.exists(OUTPUT_FILE_PATH))) { + stop("The output file ",OUTPUT_FILE_PATH, " you provided does not exists in the directory", opt$directory, "\n") +} else { + cat("Output file exists ...", OUTPUT_FILE_PATH, "\n") } # generate random string file paths - genRandomFileName <- function(prefix, file_ext = ".txt") { randStr = paste(prefix, stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"), sep = "_") @@ -531,8 +526,8 @@ output = list(lod_peaks = lod_peaks, ) output_json_data <-toJSON(output) -output_file_path = file.path(opt$directory , opt$output_file) -cat("The output file path generated is", output_file_path, "\n") + +cat("The output file path generated is", OUTPUT_FILE_PATH, "\n") cat("Writing to the output file\n") -write(output_json_data, file=output_file_path) +write(output_json_data, file=OUTPUT_FILE_PATH) |