diff options
Diffstat (limited to 'scripts/rqtl2_wrapper.R')
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 37 |
1 files changed, 21 insertions, 16 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index a6432d7..dc5955f 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -41,8 +41,8 @@ OUTPUT_FILE_PATH = file.path(opt$directory , opt$output_file) if (!(file.exists(INPUT_FILE_PATH))) { stop("The input file", INPUT_FILE_PATH, " you provided does not exists the directory", opt$directory, "\n") } else { - cat("Input file exists Reading the input file .... ", INPUT_FILE_PATH, "\n") - json_data = fromJSON(file = INPUT_FILE_PATH) + cat("Input file exists Reading the input file .... \n") + } if (!(file.exists(OUTPUT_FILE_PATH))) { stop("The output file ",OUTPUT_FILE_PATH, " you provided does not exists in the directory", opt$directory, "\n") @@ -50,22 +50,26 @@ if (!(file.exists(OUTPUT_FILE_PATH))) { 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 = +# Utility function to generate random file names of size n: +genRandomFileName <- function(prefix, string_size = 9 , file_ext = ".txt") { + randStr = paste(prefix, stri_rand_strings(1, string_size, pattern = "[A-Za-z0-9]"), sep = "_") return(paste(randStr, file_ext, sep = "")) } -# TODO work on the optional parameters e.g cores, type of computation -# TODO create temp directory for this workspace pass this as argument + + +# Step: Generate the control file name control_file_path <- file.path(opt$directory, - genRandomFileName(prefix = "control_", file_ext = ".json")) + genRandomFileName(prefix = "control", file_ext = ".json")) +cat("Generated the control file path at ", control_file_path, "\n") -cat("Generated the control file path at", control_file_path, "\n") +# Step: Reading and Parsing the input file +cat("Reading and parsing the input file \n") +json_data = fromJSON(file = INPUT_FILE_PATH) if (is.null(json_data$sep)){ cat("Using ',' as a default sep for cross file\n") json_data$sep = "," @@ -74,8 +78,6 @@ if (is.null(json_data$na.strings)){ cat("Using '-' and 'NA' as the default na.strings\n") json_data$na.strings = c("-" , "NA") } - -# use this better defaults default_keys = c( "geno_transposed", "founder_geno_transposed", "pheno_transposed" , "covar_transposed", @@ -88,6 +90,9 @@ if (!(item %in% names(json_data))){ } } + + + generate_cross_object <- function(control_file_path, json_data) { # function to write the cross object from a json data object return ( @@ -117,15 +122,13 @@ generate_cross_object <- function(control_file_path, json_data) { ) } -# generate the cross file - +# Step: generate the cross file +cat("Generating the cross object at ", control_file_path, "\n") generate_cross_object(control_file_path, json_data) -# read from the cross file path +cat("reading the cross object from", control_file_path, "\n") dataset <- read_cross2(control_file_path, quiet = FALSE) # replace this with a dynamic path - # check integrity of the cross - cat("Check the integrity of the cross object") check_cross2(dataset) if (check_cross2(dataset)) { @@ -134,6 +137,7 @@ if (check_cross2(dataset)) { print("Dataset does not meet required specifications") } + # Dataset Summarys cat("A Summary about the Dataset You Provided\n") summary(dataset) @@ -150,6 +154,7 @@ ind_ids_pheno(dataset) cat("Name of the founder Strains/n") founders(dataset) + # Function for computing the genetic probabilities perform_genetic_pr <- function(cross, cores = NO_OF_CORES, |