feat: create implementation for creating cross object using r-qtl2.

1 files changed, 110 insertions, 0 deletions

diff --git a/scripts/rqtl2_wrapper.R b/scripts/rqtl2_wrapper.R
new file mode 100644
index 0000000..30806b8
--- /dev/null
+++ b/scripts/rqtl2_wrapper.R
@@ -0,0 +1,110 @@
+# This script file contains  the an implementation of qtl mapping using r-qtl2
+# For r-qtl1 implementation see: Scripts/rqtl_wrapper.R
+# load the library
+
+library(qtl2)
+library(rjson)
+library(stringi)
+library(stringr)
+
+options(stringsAsFactors = FALSE);
+args = commandArgs(trailingOnly=TRUE)
+
+# get the json file path with pre metadata required to create the cross
+
+
+if (length(args)==0) {
+  stop("Argument for the metadata file is Missing ", call.=FALSE)
+} else {
+
+  json_file_path = args[1]
+  # convert this to an absolute file path 
+  
+}
+
+# validation for the json file 
+if (!(file.exists(json_file_path))) {
+   stop("The input file path does not exists")
+} else {
+str_glue("The input path for the metadata >>>>>>> {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="_")
+
+	return(paste(randStr,file_ext,sep=""))
+}
+
+# this should be read from the json file assigned to variables
+# TODO improve on this or use option
+
+
+crosstype <- json_data$crosstype
+geno_file <- json_data$geno_file
+pheno_file <- json_data$pheno_file
+geno_map_file <- json_data$geno_map_file 
+pheno_covar_file <- json_data$phenocovar_file
+alleles <- json_data$alleles
+
+# 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
+
+# create temp directory for this workspace 
+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 
+
+dataset <- write_control_file(control_file_path,
+    crosstype= crosstype,
+    geno_file= geno_file,
+    pheno_file= pheno_file,    
+    gmap_file= geno_map_file,
+    phenocovar_file= pheno_covar_file,
+    geno_codes=c(L=1L, C=2L),
+    alleles= alleles,    
+    na.strings=c("-", "NA"),
+    overwrite = TRUE)
+
+
+# make validation for the data
+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)){
+  print("Dataset meets required specifications for a cross")
+} else {
+  print("Dataset does not meet required specifications")
+}
+
+# Dataset Summarys 
+cat("A Summary about the Dataset You Provided\n")
+summary(dataset)
+n_ind(dataset)
+n_chr(dataset)
+cat("names of markers in the  object\n")
+marker_names(dataset)
+cat("names of phenotypes in a the object")
+pheno_names(dataset)
+cat("IDs for all individuals in the dataset cross object that have genotype data\n")
+ind_ids_geno(dataset)
+cat(" IDs for all individuals in the dataset object that have phenotype data")
+ind_ids_pheno(dataset)
+cat("Name of the founder Strains/n")
+founders(dataset)