#' @title Function to prepare the CircHunter reference annotations
#' @description This function executes the docker container circhunter by running the circRNA classification module of CircHunter starting from a set of circRNAs. For CircHunter algorithm detail please refer to: https://github.com/carlo-deintinis/circhunter/tree/master/CircHunter.
#'
#' @param group, a character string. Two options: \code{"sudo"} or \code{"docker"}, depending to which group the user belongs
#' @param scratch.folder, a character string indicating the scratch folder where docker container will be mounted
#' @param data.folder, a character string indicating the data folder where the output files will be saved
#' @param assembly, string indicating the reference human genome assembly. Compatible assemblies: hg19 (default), hg18, hg38, mm9, mm10, rn6, dm6, ce11
#' @param version, Ensembl database version used for the analysis. If no version number is provided, the last version is considered
#' @author Nicola Licheri and Giulio Ferrero
#'
#' @return Two tab-delimited tables reporting the exons and the transcript isoforms annotations of an user-selected human genome assembly
#' @examples
#'\dontrun{
#' #Download the example data
#' system("wget https://github.com/carlo-deintinis/circhunter/archive/master.zip")
#' system("unzip master.zip")
#'
#' #running the circrnaPrepareFiles function
#' circrnaPrepareFiles(group="docker", scratch.folder="/data/scratch", data.folder="/data/output", assembly="hg19")
#'
#' }
#' @export
circrnaPrepareFiles <- function(group=c("sudo","docker"), scratch.folder, data.folder, assembly="hg19", version=NULL) {
#running time 1
ptm <- proc.time()
scratch.folder <- normalizePath(scratch.folder)
data.folder <- normalizePath(data.folder)
#setting the data.folder as working folder
if (!file.exists(data.folder)) {
cat(paste("\nIt seems that the ",data.folder, " folder does not exist\n"))
return(2)
}
#storing the position of the home folder
home <- getwd()
setwd(data.folder)
#initialize status
system("echo 0 > ExitStatusFile 2>&1")
#check if scratch folder exist
if (!file.exists(scratch.folder)) {
cat(paste("\nIt seems that the ",scratch.folder, " folder does not exist\n"))
system("echo 3 > ExitStatusFile 2>&1")
setwd(data.folder)
return(3)
}
if (!(assembly %in% c("hg19", "hg18", "hg38", "mm9", "mm10", "rn6", "dm6", "ce11"))) {
cat(paste("\nThe given assembly is not supported\n"))
system("echo 2 > ExitStatusFile 2>&1")
setwd(home)
return(2)
}
#executing the docker job
params <- paste("--cidfile", paste0(data.folder, "/dockerID"),
"-v", paste0(scratch.folder, ":/scratch"),
"-v", paste0(data.folder, ":/data"),
"-d docker.io/repbioinfo/docker4circ.2019.02 Rscript /scripts/circhunter/circhunter.R",
"--preparedata ",
"-as", assembly,
"-of",
"-v", version
)
resultRun <- runDocker(group=group, params=params)
#waiting for the end of the container work
if(resultRun==0){
cat("\nThe preparation of the circRNA reference files is finished\n")
}
#running time 2
ptm <- proc.time() - ptm
dir <- dir(data.folder)
dir <- dir[grep("run.info",dir)]
if(length(dir)>0) {
con <- file("run.info", "r")
tmp.run <- readLines(con)
close(con)
tmp.run[length(tmp.run)+1] <- paste("circRNA prepare files user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("circRNA prepare files system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("circRNA prepare files elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}
else {
tmp.run <- NULL
tmp.run[1] <- paste("run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("circRNA prepare files system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("circRNA prepare files elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}
#saving log and removing docker container
container.id <- readLines(paste(data.folder,"/dockerID", sep=""), warn = FALSE)
system(paste("docker logs ", substr(container.id,1,12), " &> ",data.folder,"/circrnaPrepareFiles_", substr(container.id,1,12),".log", sep=""))
system(paste("docker rm ", container.id, sep=""))
# removing temporary files
cat("\n\nRemoving the temporary file ....\n")
system("rm -fR out.info")
system("rm -fR dockerID")
system(paste("cp ",paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
setwd(home)
}
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