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r-geno-tools-engine.R
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r-geno-tools-engine.R
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#!/usr/bin/env Rscript
# Author: Julien Diot [email protected]
# Tue 24 Aug 2021 The University of Tokyo
#
# Description:
# Main script of R-geno-tools-enigne
options(keep.source = TRUE) # to get the error locations
ERROR_AS_JSON <- FALSE
if (nzchar(Sys.getenv("RGENOROOT"))) {
projectRoot <- Sys.getenv("RGENOROOT")
} else {
projectRoot <- getwd()
}
if ("renv" %in% rownames(installed.packages()) && !isTRUE(as.logical(Sys.getenv("NO_RENV")))) {
renv::load(projectRoot)
}
withCallingHandlers(
engineError = function(err) {
if (ERROR_AS_JSON) {
jsonErr <- jsonlite::toJSON(list(message = err$message,
extra = err$extra),
auto_unbox = TRUE)
write(jsonErr, stderr())
q("no", status = 42)
} else {
stop(err)
}
}, error = function(err) {
if (ERROR_AS_JSON) {
# extract stack-trace:
error_locations <- limitedLabels(sys.calls())
error_locations <- error_locations[-1] # drop 1st
error_locations[1] <- paste0("r-geno-tools-engine.R", error_locations[1])
start_with_R_file <- grepl("^[\\w,\\s-]+\\.[Rr]", error_locations, perl = TRUE)
error_locations <- error_locations[start_with_R_file]
last_loc <- error_locations[length(error_locations)]
last_fun <- regmatches(last_loc,
gregexec("^.*: ([\\w.]+)\\(",
last_loc,
perl = TRUE
))[[1]][2,1] # extract catching group
if (last_fun == ".handleSimpleError") {
last_loc <- gsub("\\.handleSimpleError.*", replacement = deparse(err$call) , last_loc)
}
error_locations[length(error_locations)] <- last_loc
error_locations <- paste0(error_locations, collapse = "\n")
# write error info in json
jsonErr = jsonlite::toJSON(list(message = err$message,
extra = list(
"code" = "UNEXPECTED_ERROR",
"stacktrace" = error_locations)),
auto_unbox = TRUE)
write(jsonErr, stderr())
q("no", status = 42)
} else {
stop(err)
}
}, warning = function(warn){
# catch warnings and send them to stdout instead of stderr
cat("-- WARNING -- ", warn$message, "\n")
rlang::cnd_muffle(warn)
},
{
# Create parser ----
library(argparse)
formatter_class <- "lambda prog: argparse.RawTextHelpFormatter(prog, max_help_position=42, width=100)"
main_parser = ArgumentParser(
prog = 'r-geno-tools-engine',
description = "Toolbox for some genomic analysis written in R.",
formatter_class = formatter_class,
# argument_default = "True",
usage = "%(prog)s"
)
main_subparsers = main_parser$add_subparsers(prog = 'r-geno-tools-engine',
title = "Available commands",
dest = "command")
# load argument descriptions
source(file.path(projectRoot, 'src/commandArgs.R'))
parserList <- c() # to keep names of subcommands
## GWAS gwas ----
gwas_parser = main_subparsers$add_parser("gwas",
help = "Do a gwas analysis",
description = "Run a GWAS analysis",
formatter_class = formatter_class,
argument_default = "True")
gwas_parser$add_argument(arg$genoFile$flag,
help = arg$genoFile$help,
type = arg$genoFile$type,
required = TRUE)
gwas_parser$add_argument(arg$phenoFile$flag,
help = arg$phenoFile$help,
type = arg$phenoFile$type,
required = TRUE)
gwas_parser$add_argument(arg$trait$flag,
help = arg$trait$help,
type = arg$trait$type,
required = TRUE)
gwas_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
gwas_parser$add_argument(arg$test$flag,
help = arg$test$help,
type = arg$test$type,
default = arg$test$default)
gwas_parser$add_argument(arg$fixed$flag,
help = arg$fixed$help,
type = arg$fixed$type,
default = arg$fixed$default)
gwas_parser$add_argument(arg$response$flag,
help = arg$response$help,
type = arg$response$type,
default = arg$response$default)
gwas_parser$add_argument(arg$thresh_maf$flag,
help = arg$thresh_maf$help,
type = arg$thresh_maf$type,
default = arg$thresh_maf$default)
gwas_parser$add_argument(arg$thresh_callrate$flag,
help = arg$thresh_callrate$help,
type = arg$thresh_callrate$type,
default = arg$thresh_callrate$default)
gwas_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## GWAS manplot ----
manplot_parser = main_subparsers$add_parser("gwas-manplot",
help = "Draw a Manhattan Plot",
description = "Draw a Manhattan Plot",
formatter_class=formatter_class)
manplot_parser$add_argument(arg$gwasFile$flag,
help = arg$gwasFile$help,
type = arg$gwasFile$type,
required = TRUE)
manplot_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
manplot_parser$add_argument(arg$adj_method$flag,
help = arg$adj_method$help,
type = arg$adj_method$type,
default = arg$adj_method$default)
manplot_parser$add_argument(arg$thresh_p$flag,
help = arg$thresh_p$help,
type = arg$thresh_p$type,
default = arg$thresh_p$default)
manplot_parser$add_argument(arg$chr$flag,
help = arg$chr$help,
type = arg$chr$type,
default = arg$chr$default)
manplot_parser$add_argument(arg$no_interactive$flag,
help = arg$no_interactive$help,
action = 'store_true')
manplot_parser$add_argument(arg$filter_pAdj$flag,
help = arg$filter_pAdj$help,
type = arg$filter_pAdj$type,
default = arg$filter_pAdj$default)
manplot_parser$add_argument(arg$filter_nPoints$flag,
help = arg$filter_nPoints$help,
type = arg$filter_nPoints$type,
default = arg$filter_nPoints$default)
manplot_parser$add_argument(arg$filter_quant$flag,
help = arg$filter_quant$help,
type = arg$filter_quant$type,
default = arg$filter_quant$default)
manplot_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## GWAS adjResults ----
adjResults_parser = main_subparsers$add_parser("gwas-adjresults",
help = "Adjust GWAS p-values",
description = "Adjust GWAS p-values and filter the results",
formatter_class=formatter_class)
adjResults_parser$add_argument(arg$gwasFile$flag,
help = arg$gwasFile$help,
type = arg$gwasFile$type,
required = TRUE)
adjResults_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
adjResults_parser$add_argument(arg$adj_method$flag,
help = arg$adj_method$help,
type = arg$adj_method$type,
default = arg$adj_method$default)
adjResults_parser$add_argument(arg$filter_pAdj$flag,
help = arg$filter_pAdj$help,
type = arg$filter_pAdj$type,
default = arg$filter_pAdj$default)
adjResults_parser$add_argument(arg$filter_nPoints$flag,
help = arg$filter_nPoints$help,
type = arg$filter_nPoints$type,
default = arg$filter_nPoints$default)
adjResults_parser$add_argument(arg$filter_quant$flag,
help = arg$filter_quant$help,
type = arg$filter_quant$type,
default = arg$filter_quant$default)
adjResults_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## LDplot ----
ldplot_parser = main_subparsers$add_parser("ldplot",
help = "Get plot of the linkage disequilibrium between consecutive markers",
description = "Get plot of the linkage disequilibrium between consecutive markers",
formatter_class=formatter_class)
ldplot_parser$add_argument(arg$genoFile$flag,
help = arg$genoFile$help,
type = arg$genoFile$type,
required = TRUE)
ldplot_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
ldplot_parser$add_argument(arg$from$flag,
help = arg$from$help,
type = arg$from$type,
required = TRUE)
ldplot_parser$add_argument(arg$to$flag,
help = arg$to$help,
type = arg$to$type,
required = TRUE)
ldplot_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## relmat pedigree ----
pedRelMat_parser = main_subparsers$add_parser("relmat-ped",
help = "Pedigree relationship matrix",
description = "Caclulate a pedigree relationship matrix.\\n\\nThe output file shoud end by either `.csv` or `.json`.",
formatter_class=formatter_class)
pedRelMat_parser$add_argument(arg$pedFile$flag,
help = arg$pedFile$help,
type = arg$pedFile$type,
required = TRUE)
pedRelMat_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
pedRelMat_parser$add_argument(arg$u_string$flag,
help = arg$u_string$help,
type = arg$u_string$type,
default = arg$u_string$default)
pedRelMat_parser$add_argument(arg$no_header$flag,
help = arg$no_header$help,
action = 'store_true')
pedRelMat_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## relmat genomic ----
genoRelMat_parser = main_subparsers$add_parser("relmat-geno",
help = "Genomic relationship matrix",
description = "Caclulate a genomic relationship matrix.\\n\\nThe output file shoud end by either `.csv` or `.json`.",
formatter_class=formatter_class)
genoRelMat_parser$add_argument(arg$genoFile$flag,
help = arg$genoFile$help,
type = arg$genoFile$type,
required = TRUE)
genoRelMat_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
genoRelMat_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## relmat combined ----
combinedRelMat_parser = main_subparsers$add_parser(
"relmat-combined",
help = "Combined relationship matrix",
description = paste(
"Correct a pedigree relationship matrix using a genomic relationship matrix.",
"\\n\\nThe output file shoud end by either `.csv` or `.json`.",
"\\n\\nIndividuals in the genomic relationship matrix which do not belong ",
"to the pedigree relationship matrix will be ignored.",
"\\n\\nRefference of the method can be found at:",
"\\n\t- \"Martini, JW, et al. 2018 The effect of the H-1 scaling factors tau and omega on the structure of H in the single-step procedure. Genetics Selection Evolution 50(1), 16\"",
"\\n\t-\"Legarra, A, et al. 2009 A relationship matrix including full pedigree and genomic information. Journal of Dairy Science 92, 4656–4663\"",
"\\n \\n \\n "),
formatter_class=formatter_class)
combinedRelMat_parser$add_argument(arg$ped_relmatFile$flag,
help = arg$ped_relmatFile$help,
type = arg$ped_relmatFile$type,
required = TRUE)
combinedRelMat_parser$add_argument(arg$geno_relmatFile$flag,
help = arg$geno_relmatFile$help,
type = arg$geno_relmatFile$type,
required = TRUE)
combinedRelMat_parser$add_argument(arg$combine_method$flag,
help = arg$combine_method$help,
type = arg$combine_method$type,
required = TRUE)
combinedRelMat_parser$add_argument(arg$tau$flag,
help = arg$tau$help,
type = arg$tau$type)
combinedRelMat_parser$add_argument(arg$omega$flag,
help = arg$omega$help,
type = arg$omega$type)
combinedRelMat_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
combinedRelMat_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## relmat heatmap ----
relMatHeat_parser = main_subparsers$add_parser("relmat-heatmap",
help = "Draw a heatmap of a relationship matrix",
description = "Draw a heatmap of a relationship matrix",
formatter_class=formatter_class)
relMatHeat_parser$add_argument(arg$relmatFile$flag,
help = arg$relmatFile$help,
type = arg$relmatFile$type,
required = TRUE)
relMatHeat_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
relMatHeat_parser$add_argument(arg$no_interactive$flag,
help = arg$no_interactive$help,
action = 'store_true')
relMatHeat_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## pedNetwork ----
pedNet_parser = main_subparsers$add_parser("pedNetwork",
help = "Draw interactive pedigree network",
description = "Draw interactive pedigree network",
formatter_class=formatter_class)
pedNet_parser$add_argument(arg$pedFile$flag,
help = arg$pedFile$help,
type = arg$pedFile$type,
required = TRUE)
pedNet_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
pedNet_parser$add_argument(arg$u_string$flag,
help = arg$u_string$help,
type = arg$u_string$type,
default = arg$u_string$default)
pedNet_parser$add_argument(arg$no_header$flag,
help = arg$no_header$help,
action = 'store_true')
pedNet_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## crossing-simulation ----
crossSim_parser = main_subparsers$add_parser("crossing-simulation",
help = "Simulate crossing between individuals",
description = paste(
"Simulate the cross",
"specified in the crossing",
"table and write the simulated",
"genotypes in a phased `.vcf.gz`",
"file. This command will return",
"the path of the created file"),
formatter_class = formatter_class)
crossSim_parser$add_argument(arg$phasedGenoFile$flag,
help = arg$phasedGenoFile$help,
type = arg$phasedGenoFile$type,
required = TRUE)
crossSim_parser$add_argument(arg$crossTableFile$flag,
help = arg$crossTableFile$help,
type = arg$crossTableFile$type,
required = TRUE)
crossSim_parser$add_argument(arg$SNPcoordFile$flag,
help = arg$SNPcoordFile$help,
type = arg$SNPcoordFile$type,
default = NULL)
# required = TRUE)
crossSim_parser$add_argument(arg$nCross$flag,
help = arg$nCross$help,
type = arg$nCross$type,
default = arg$nCross$default)
crossSim_parser$add_argument(arg$outGenoFile$flag,
help = arg$outGenoFile$help,
type = arg$outGenoFile$type,
required = TRUE)
crossSim_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## progeny-blup-calculation ----
prog_blup_parser = main_subparsers$add_parser(
"progeny-blup-calculation",
help = "Estimate progenies' BLUPs of given crosses",
description = paste(
"Estimate the BLUPs' expected value and variance of the progenies of a",
"given crosses specifyed in the crossing table. The results are written in",
"a `.json` file."
),
formatter_class = formatter_class)
prog_blup_parser$add_argument(arg$phasedGenoFile$flag,
help = arg$phasedGenoFile$help,
type = arg$phasedGenoFile$type,
required = TRUE)
prog_blup_parser$add_argument(arg$crossTableFile$flag,
help = arg$crossTableFile$help,
type = arg$crossTableFile$type,
required = TRUE)
prog_blup_parser$add_argument(arg$SNPcoordFile$flag,
help = arg$SNPcoordFile$help,
type = arg$SNPcoordFile$type,
required = TRUE)
prog_blup_parser$add_argument(arg$markersEffectsFile$flag,
help = arg$markersEffectsFile$help,
type = arg$markersEffectsFile$type,
required = TRUE)
prog_blup_parser$add_argument(arg$outProgBlupFile$flag,
help = arg$outProgBlupFile$help,
type = arg$outProgBlupFile$type,
required = TRUE)
prog_blup_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## progeny-blup-plot ----
prog_blup_plot = main_subparsers$add_parser(
"progeny-blup-plot",
help = "Draw a plot of the progenies BLUPs' expected values with error bars",
description = paste(
"Draw a plot of the progenies BLUPs' expected values with error bars.",
"X axis is the crosses, and Y axis the blups. The points are located",
"at the expected value and the error bar length is the standard deviation."
),
formatter_class = formatter_class)
prog_blup_plot$add_argument(arg$progeniesBlupFile$flag,
help = arg$progeniesBlupFile$help,
type = arg$progeniesBlupFile$type,
required = TRUE)
prog_blup_plot$add_argument(arg$sorting$flag,
help = arg$sorting$help,
type = arg$sorting$type,
default = arg$sorting$default)
prog_blup_plot$add_argument(arg$errorBarInterval$flag,
help = arg$errorBarInterval$help,
type = arg$errorBarInterval$type,
default = arg$errorBarInterval$default)
prog_blup_plot$add_argument(arg$y_axisName$flag,
help = arg$y_axisName$help,
type = arg$y_axisName$type,
default = arg$y_axisName$default)
prog_blup_plot$add_argument(arg$trait$flag,
help = arg$trait$help,
type = arg$trait$type,
default = "")
prog_blup_plot$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
prog_blup_plot$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## progeny-blup-plot-2-traits ----
prog_blup_plot_2_traits = main_subparsers$add_parser(
"progeny-blup-plot-2-traits",
help = "Draw a plot of the progenies BLUPs' expected values for 2 traits with prediction ellipses",
description = paste(
"Draw a plot of the progenies BLUPs' expected values with prediction ellipses.",
"The points are located at the expected value and the ellipses",
"size represent the `--confidenceLevel` prediction interval (default 95%)."
),
formatter_class = formatter_class)
prog_blup_plot_2_traits$add_argument(arg$progeniesBlupFile$flag,
help = arg$progeniesBlupFile$help,
type = arg$progeniesBlupFile$type,
required = TRUE)
prog_blup_plot_2_traits$add_argument(arg$x_trait$flag,
help = arg$x_trait$help,
type = arg$x_trait$type,
required = TRUE)
prog_blup_plot_2_traits$add_argument(arg$y_trait$flag,
help = arg$y_trait$help,
type = arg$y_trait$type,
required = TRUE)
prog_blup_plot_2_traits$add_argument(arg$confidenceLevel$flag,
help = arg$confidenceLevel$help,
type = arg$confidenceLevel$type,
default = arg$confidenceLevel$default)
prog_blup_plot_2_traits$add_argument(arg$x_suffix$flag,
help = arg$x_suffix$help,
type = arg$x_suffix$type,
default = arg$x_suffix$default)
prog_blup_plot_2_traits$add_argument(arg$y_suffix$flag,
help = arg$y_suffix$help,
type = arg$y_suffix$type,
default = arg$y_suffix$default)
prog_blup_plot_2_traits$add_argument(arg$ellipses_npoints$flag,
help = arg$ellipses_npoints$help,
type = arg$ellipses_npoints$type,
default = arg$ellipses_npoints$default)
prog_blup_plot_2_traits$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
prog_blup_plot_2_traits$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## GS model evaluation ----
gs_model_evaluation_parser = main_subparsers$add_parser(
"evaluate-gs-model",
help = "Evaluate a genomic selection model.",
description = paste(
"Evaluate a genomic selection model.",
"This evaluation is done with a repeated cross-validation."
),
formatter_class = formatter_class)
gs_model_evaluation_parser$add_argument(arg$genoFile$flag,
help = arg$genoFile$help,
type = arg$genoFile$type,
required = TRUE)
gs_model_evaluation_parser$add_argument(arg$phenoFile$flag,
help = arg$phenoFile$help,
type = arg$phenoFile$type,
required = TRUE)
gs_model_evaluation_parser$add_argument(arg$trait$flag,
help = arg$trait$help,
type = arg$trait$type,
required = TRUE)
gs_model_evaluation_parser$add_argument(arg$with_dominance$flag,
help = arg$with_dominance$help,
type = arg$with_dominance$type,
required = TRUE)
gs_model_evaluation_parser$add_argument(arg$n_folds$flag,
help = arg$n_folds$help,
type = arg$n_folds$type,
default = arg$n_folds$default)
gs_model_evaluation_parser$add_argument(arg$n_repetitions$flag,
help = arg$n_repetitions$help,
type = arg$n_repetitions$type,
default = arg$n_repetitions$default)
gs_model_evaluation_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
gs_model_evaluation_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## plot-gs-model-evaluation ----
plot_gs_model_evaluation_parser = main_subparsers$add_parser(
"plot-gs-model-evaluation",
help = "Create an interactive plot of the evaluation resutls",
description = paste(
"Create an interactive plot of the evaluation resutls"
),
formatter_class = formatter_class)
plot_gs_model_evaluation_parser$add_argument(arg$evaluation_file$flag,
help = arg$evaluation_file$help,
type = arg$evaluation_file$type,
required = TRUE)
plot_gs_model_evaluation_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
plot_gs_model_evaluation_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## Train GS model ----
train_gs_model_parser = main_subparsers$add_parser(
"train-gs-model",
help = "Train a genomic selection model.",
description = paste(
"Train a genomic selection model.",
"This model allow to include optionnaly dominance effects.",
"The result file will contain the estimated markers effects that can",
"be used to make predictions."
),
formatter_class = formatter_class)
train_gs_model_parser$add_argument(arg$genoFile$flag,
help = arg$genoFile$help,
type = arg$genoFile$type,
required = TRUE)
train_gs_model_parser$add_argument(arg$phenoFile$flag,
help = arg$phenoFile$help,
type = arg$phenoFile$type,
required = TRUE)
train_gs_model_parser$add_argument(arg$trait$flag,
help = arg$trait$help,
type = arg$trait$type,
required = TRUE)
train_gs_model_parser$add_argument(arg$with_dominance$flag,
help = arg$with_dominance$help,
type = arg$with_dominance$type,
required = TRUE)
train_gs_model_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
train_gs_model_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
## gs-predictions ----
gs_prediction_parser = main_subparsers$add_parser(
"gs-predictions",
help = "Make phenotypic prediction using a markers effects",
description = paste(
"Make phenotypic prediction using markers effects"
),
formatter_class = formatter_class)
gs_prediction_parser$add_argument(arg$genoFile$flag,
help = arg$genoFile$help,
type = arg$genoFile$type,
required = TRUE)
gs_prediction_parser$add_argument(arg$markersEffectsFile$flag,
help = arg$markersEffectsFile$help,
type = arg$markersEffectsFile$type,
required = TRUE)
gs_prediction_parser$add_argument(arg$outFile$flag,
help = arg$outFile$help,
type = arg$outFile$type,
required = TRUE)
gs_prediction_parser$add_argument(arg$json_error$flag,
help = arg$json_error$help,
default = arg$json_error$default,
action = 'store_true',
required = FALSE)
# Parse the command line arguments
args = main_parser$parse_args()
# show help if no command is provided
if (is.null(args$command)) {
main_parser$print_help()
quit(save = "no", status = 0)
}
ERROR_AS_JSON <- args$json_errors
# log input parameters
time <- as.character(Sys.time())
cat(time, 'call to R-geno-engine.R:\n', paste0(names(args), ' = ', args, '\n'))
# load engine's R packages dependencies:
suppressPackageStartupMessages({
library(R6) # R object oriented
})
# source R functions:
invisible(
sapply(FUN = source,
X = list.files(file.path(projectRoot, "src"), pattern = ".R$", full.names = T))
)
if (args$command == "gwas") {
# gwas ----
gwas_results <- run_gwas(genoFile = args$genoFile,
phenoFile = args$phenoFile,
trait = args$trait,
test = args$test,
fixed = args$fixed,
response = args$response,
thresh_maf = args$thresh_maf,
thresh_callrate = args$thresh_callrate,
outFile = args$outFile)
quit(save = "no", status = 0)
} else if (args$command == "gwas-manplot") {
# gwas-manplot ----
if (identical(args$chr, '')) {
args$chr <- NA
}
p <- draw_manhattanPlot(gwasFile = args$gwasFile,
adj_method = args$adj_method,
thresh_p = args$thresh_p,
chr = args$chr,
interactive = !args$no_interactive,
filter_pAdj = args$filter_pAdj,
filter_nPoints = args$filter_nPoints,
filter_quant = args$filter_quant,
outFile = args$outFile)
quit(save = "no", status = 0)
} else if (args$command == "gwas-adjresults") {
# gwas-adjresults ----
gwas_adj <- run_resAdjustment(gwasFile = args$gwasFile,
gwasUrl = args$gwasUrl,
adj_method = args$adj_method,
filter_pAdj = args$filter_pAdj,
filter_nPoints = args$filter_nPoints,
filter_quant = args$filter_quant,
outFile = args$outFile)
quit(save = "no", status = 0)
} else if (args$command == "ldplot") {
# ldplot ----
imgFile <- draw_ldPlot(genoFile = args$genoFile,
from = args$from,
to = args$to,
outFile = args$outFile)
quit(save = "no", status = 0)
} else if (args$command == "relmat-ped") {
# relmat-ped ----
relMat <- calc_pedRelMat(pedFile = args$pedFile,
unknown_string = args$unknown_string,
header = !args$no_header,
outFile = args$outFile)
quit(save = 'no', status = 0)
} else if (args$command == "relmat-geno") {
# relmat-geno ----
relMat <- calc_genoRelMat(genoFile = args$genoFile,
outFile = args$outFile)
quit(save = 'no', status = 0)
} else if (args$command == "relmat-combined") {
# relmat-combined ----
relMat <- calc_combinedRelMat(pedRelMatFile = args$ped_relmatFile,
genoRelMatFile = args$geno_relmatFile,
method = args$combine_method,
tau = args$tau,
omega = args$omega,
outFile = args$outFile)
quit(save = 'no', status = 0)
} else if (args$command == 'relmat-heatmap') {
# relmat-heatmap ----
p <- draw_relHeatmap(relMatFile = args$relmatFile,
interactive = !args$no_interactive,
outFile = args$outFile)
quit(save = "no", status = 0)
} else if (args$command == 'pedNetwork') {
# pedNetwork ----
p <- draw_pedNetwork(pedFile = args$pedFile,
unknown_string = args$unknown_string,
header = !args$no_header,
outFile = args$outFile)
quit(save = "no", status = 0)
} else if (args$command == 'crossing-simulation') {
# crossing-simulation ----
outFile <- crossingSimulation(genoFile = args$genoFile,
crossTableFile = args$crossTableFile,
SNPcoordFile = args$SNPcoordFile,
nCross = args$nCross,
outFile = args$outFile)
cat(outFile)
quit(save = "no", status = 0)
} else if (args$command == 'progeny-blup-calculation') {
# progeny-blup-calculation ----
progBlups <- calc_progenyBlupEstimation(
genoFile = args$genoFile,
crossTableFile = args$crossTableFile,
SNPcoordFile = args$SNPcoordFile,
markerEffectsFile = args$markerEffectsFile,
outFile = args$outFile
)
quit(save = "no", status = 0)
} else if (args$command == 'progeny-blup-plot') {
# progeny-blup-plot ----
if (identical(args$trait, "")) {
args$trait <- NULL
}
p <- draw_progBlupsPlot(
progEstimFile = args$progeniesBlupFile,
sorting = args$sorting,
errorBarInterval = args$error_bar_interval,
y_axisName = args$y_axis_name,
trait = args$trait,
outFile = args$outFile
)
quit(save = "no", status = 0)
} else if (args$command == 'progeny-blup-plot-2-traits') {
# progeny-blup-plot-2-traits ----
if (identical(args$trait, "")) {
args$trait <- NULL
}
p <- draw_progBlupsPlot_2traits(
progEstimFile = args$progeniesBlupFile,
x_trait = args$x_trait,
y_trait = args$y_trait,
confidenceLevel = args$confidence_level,
x_suffix = args$x_suffix,
y_suffix = args$y_suffix,
ellipses_npoints = args$ellipses_npoints,
outFile = args$outFile
)
quit(save = "no", status = 0)
} else if (args$command == 'evaluate-gs-model') {
# evaluate-gs-model ----
evaluation <- cross_validation_evaluation_main(genoFile = args$geno,
phenoFile = args$pheno,
trait = args$trait,
with_dominance = args$with_dominance,
n_folds = args$n_folds,
n_repetitions = args$n_repetitions,
thresh_maf = 0,
outFile = args$outFile)
quit(save = "no", status = 0)
} else if (args$command == 'plot-gs-model-evaluation') {
# plot-gs-model-evaluation ----
plot <- draw_evaluation_plot(evaluationFile = args$evaluation_file,
outFile = args$outFile)
quit(save = "no", status = 0)
} else if (args$command == 'train-gs-model') {
# train-gs-model ----
model <- train_gs_model_main(genoFile = args$geno,
phenoFile = args$pheno,
trait = args$trait,
with_dominance = args$with_dominance,
thresh_maf = 0,
outFile = args$outFile)
quit(save = "no", status = 0)
} else if (args$command == 'gs-predictions') {
# gs-predictions ----
predictions <- predict_gs_model_main(genoFile = args$geno,
markerEffectsFile = args$markerEffectsFile,
outFile = args$outFile)
quit(save = "no", status = 0)
}
# Should not arrive here.
quit(save = "no", status = 1)
})