#' @title Running xenome, https://github.com/data61/gossamer/
#' @description This function executes the docker container bwa1 where BWA is installed BWA is a read alignment package that efficiently align short sequencing reads against a large reference sequence This aligner provides optimal results with DNA-seq data
#'
#' @param group, a character string. Two options: \code{"sudo"} or \code{"docker"}, depending to which group the user belongs
#' @param fastq.folder, a character string indicating where gzip fastq files are located
#' @param scratch.folder, a character string indicating the scratch folder where docker container will be mounted
#' @param xenome.folder, a character string indicating the folder where the indexed reference genomes generated by xenome are locates
#' @param seq.type, a character string indicating the type of reads to be trimmed. Two options: \code{"se"} or \code{"pe"} respectively for single end and pair end sequencing
#' @param threads, a number indicating the number of cores to be used from the application
#' @author Raffaele Calogero
#'
#' @return ambiguous, both, neither, hs and mm fastq.gz files. xeno_hs_R1.fastq.gz and xeno_hs_R2.fastq.gz are fastq file free of mouse reads and are used for further analysis.
#' @examples
#'\dontrun{
#' #downloading examples 1 million reads of mcf7 exome mixed with 1 million of mouse derived by human exome capturing
#' system("wget http://130.192.119.59/public/hs1m_mm1m_R1.fastq.gz")
#' system("wget http://130.192.119.59/public/hs1m_mm1m_R2.fastq.gz")
#' #running xenome
#' xenome(group="docker",fastq.folder=getwd(), scratch.folder="/data/scratch",
#' xenome.folder="/data/scratch/hg19.mm10", seq.type="pe",
#' threads=24)
#'
#' }
#' @export
xenome <- function(group=c("sudo","docker"),fastq.folder=getwd(), scratch.folder="/data/scratch", xenome.folder, seq.type="pe", threads=1){
home <- getwd()
setwd(fastq.folder)
#initialize status
system("echo 0 > ExitStatusFile 2>&1")
#running time 1
ptm <- proc.time()
#running time 1
test <- dockerTest()
if(!test){
cat("\nERROR: Docker seems not to be installed in your system\n")
system("echo 10 > ExitStatusFile 2>&1")
setwd(home)
return(10)
}
#########check 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(home)
return(3)
}
#############################################
tmp.folder <- gsub(":","-",gsub(" ","-",date()))
scrat_tmp.folder=file.path(scratch.folder, tmp.folder)
writeLines(scrat_tmp.folder,paste(fastq.folder,"/tempFolderID", sep=""))
cat("\ncreating a folder in scratch folder\n")
dir.create(file.path(scratch.folder, tmp.folder))
dir.create(file.path(scratch.folder, tmp.folder,"/tmp"))
dir <- dir(path=fastq.folder)
dir.info <- dir[which(dir=="run.info")]
if(length(dir.info)>0){
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
system(paste("cp ",fastq.folder,"/run.info ", scratch.folder,"/",tmp.folder,"/run.info", sep=""))
}
dir <- dir[grep(".fastq.gz$", dir)]
cat("\ncopying \n")
if(length(dir)==0){
cat(paste("It seems that in ", fastq.folder, "there are not fastq.gz files"))
system("echo 1 > ExitStatusFile 2>&1")
setwd(home)
return(1)
}else if(length(dir)>2){
cat(paste("It seems that in ", fastq.folder, "there are more than two fastq.gz files"))
system("echo 2 > ExitStatusFile 2>&1")
setwd(home)
return(2)
}else if(length(dir)==2 & seq.type=="pe"){
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
system(paste("cp ",fastq.folder,"/",dir[1], " ",scratch.folder,"/",tmp.folder,"/data_R1.fastq.gz", sep=""))
system(paste("cp ",fastq.folder,"/",dir[2], " ",scratch.folder,"/",tmp.folder,"/data_R2.fastq.gz", sep=""))
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
}else if(length(dir)==1 & seq.type=="se"){
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
system(paste("cp ",fastq.folder,"/",dir[1], " ",scratch.folder,"/",tmp.folder,"/data_R1.fastq.gz", sep=""))
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
}
#fastq linking fpr docker
docker_fastq.folder=file.path(scratch.folder, tmp.folder)
cat("\nsetting as working dir the scratch folder and running xenome docker container\n")
if(seq.type=="pe"){
if(group=="sudo"){
params <- paste("--cidfile ",fastq.folder,"/dockerID -v ",docker_fastq.folder,":/data/scratch -v ",xenome.folder,":/xenome -d docker.io/repbioinfo/xenome.2017.01 sh /bin/xenome_pe.sh ", threads," ",fastq.folder, sep="")
resultRun <- runDocker(group="sudo", params=params)
}else{
params <- paste("--cidfile ",fastq.folder,"/dockerID -v ",docker_fastq.folder,":/data/scratch -v ",xenome.folder,":/xenome -d docker.io/repbioinfo/xenome.2017.01 sh /bin/xenome_pe.sh ", threads," ",fastq.folder, sep="")
resultRun <- runDocker(group="docker", params=params)
}
}else if(seq.type=="se"){
if(group=="sudo"){
params <- paste("--cidfile ",fastq.folder,"/dockerID -v ",docker_fastq.folder,":/data/scratch -v ",xenome.folder,":/xenome -d docker.io/repbioinfo/xenome.2017.01 sh /bin/xenome_se.sh ", threads," ",fastq.folder, sep="")
resultRun <- runDocker(group="sudo", params=params)
}else{
params <- paste("--cidfile ",fastq.folder,"/dockerID -v ",docker_fastq.folder,":/data/scratch -v ",xenome.folder,":/xenome -d docker.io/repbioinfo/xenome.2017.01 sh /bin/xenome_se.sh ", threads," ",fastq.folder, sep="")
resultRun <- runDocker(group="docker", params=params)
}
}
if(resultRun==0){
system(paste("cp -R ", docker_fastq.folder, "/* ", fastq.folder, sep=""))
}
#running time 2
ptm <- proc.time() - ptm
con <- file(paste(fastq.folder,"run.info", sep="/"), "r")
tmp.run <- readLines(con)
close(con)
tmp.run[length(tmp.run)+1] <- paste("user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,paste(fastq.folder,"run.info", sep="/"))
#saving log and removing docker container
container.id <- readLines(paste(fastq.folder,"/dockerID", sep=""), warn = FALSE)
# system(paste("docker logs ", container.id, " >& ", substr(container.id,1,12),".log", sep=""))
system(paste("docker logs ", container.id, " >& ","xenome_",substr(container.id,1,12),".log", sep=""))
system(paste("docker rm ", container.id, sep=""))
#removing temporary folder
cat("\n\nRemoving the xenome temporary file ....\n")
system(paste("rm -R ",docker_fastq.folder))
system(paste("rm -f ",fastq.folder,"/dockerID", sep=""))
system(paste("rm -f ",fastq.folder,"/tempFolderID", sep=""))
system(paste("cp ",paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")," ",fastq.folder, sep=""))
setwd(home)
}
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