diff options
| -rw-r--r-- | scripts/rqtl2_wrapper.R | 87 |
1 files changed, 10 insertions, 77 deletions
diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R index db4797a..bd5b302 100644 --- a/scripts/rqtl2_wrapper.R +++ b/scripts/rqtl2_wrapper.R @@ -30,8 +30,6 @@ if (!(file.exists(json_file_path))) { json_data = fromJSON(file = json_file_path) } - - # generate random string file path here genRandomFileName <- function(prefix, file_ext = ".txt") { randStr = paste(prefix, stri_rand_strings(1, 9, pattern = "[A-Za-z0-9]"), sep = @@ -39,18 +37,8 @@ genRandomFileName <- function(prefix, file_ext = ".txt") { return(paste(randStr, file_ext, sep = "")) } - - # TODO work on the optional parameters -# better fit for reading the data -# make validations - -# parsing the required data for example the geno_codes - - -# geno_codes handle the geno codes here - # make assertion for the geno_file and the geno_file exists # make assertion for the physical map file or the geno map file exists @@ -59,87 +47,32 @@ control_file_path <- file.path("/home/kabui", genRandomFileName(prefix = "control_", file_ext = ".json")) str_glue("Generated control file path is {control_file_path}") - - - -# create the cross file here from the arguments provided -# todo add more validation checks here - -# issue I can no define the different paths for files for example pheno_file - -# think about the issue about geno codes ~~~~ -# function to generate a cross file from a json list - - - -# work on the default from the json_data validation here # better defaults for the json file - - -json_data - -json_data$na_strings - - if (is.null(json_data$sep)){ cat("Using ',' as a default sep for cross file\n") json_data$sep = "," } - if (is.null(json_data$na.strings)){ cat("Using '-' and 'NA' as the default na.strings\n") json_data$na.strings = c("-" , "NA") } -if (is.null(json_data$geno_transposed)) { -cat("Using FALSE as default parameter for geno_transposed\n") -json_data$geno_transposed = FALSE -} - -if (is.null(json_data$founder_geno_transposed)){ -cat("Using FALSE as default parameter for founder_geno_transposed\n") -json_data$founder_geno_transposed = FALSE -} - - -if (is.null(json_data$pheno_transposed)) { -cat("Using FALSE as default parameter for pheno_transposed\n") -json_data$geno_transposed = FALSE -} - +# use this better defaults +default_keys = c( + "geno_transposed", "founder_geno_transposed", + "pheno_transposed" , "covar_transposed", + "phenocovar_transposed") -if( is.null(json_data$covar_transposed) ){ -cat("Using FALSE as default parameter for covar_transposed\n") -json_data$covar_transposed = FALSE +for (item in default_keys) { +if (!(item %in% names(json_data))){ + cat("Using FALSE as default parameter for ", item) + cat("\n") + json_data[item] = FALSE } - - -if (is.null(json_data$phenocovar_transposed)){ -cat("Using FALSE as default parameter for phenocovar_transposed\n") -json_data$phenocovar_transposed = FALSE } - -# probably check on using a dict for check this parameter -# more like default object parameter - - -cross_default1 <- c( - "sep" = ",", - "na_strings" = c("-", "NA"), - "geno_transposed" = FALSE, - "covar_transposed" = FALSE, - "pheno_transposed" = FALSE, - "founder_geno_transposed" = FALSE, - "phenocovar_transposed" = FALSE - -) - - - -# mssing something here generate_cross_object <- function(json_data) { # function to write the cross object from a json data object return ( |