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# 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)
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