#' @title A function to execute seqtk trimming
#' @description This function executes a ubuntu docker that remove reads shorter of a specific threshold
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param scratch.folder, a character string indicating the path of the scratch folder
#' @param data.folder, a character string indicating the folder where input data are located and where output will be written
#' @param min.length, min nucleotide lenght of each fasta seq
#'
#' @author Raffaele A Calogero, raffaele.calogero [at] unito [dot] it, University of Torino. Italy
#'
#' @return Returns a fasta file colled trimmed.fasta.gz
#' @examples
#' \dontrun{
#' #running fastq2fasta
#' trimfasta(group="docker", scratch.folder="/data/scratch", data.folder=getwd(), min.length=300)
#' }
#'
#' @export
trimFasta <- function(group=c("sudo","docker"), scratch.folder, data.folder, min.length=300){
#running time 1
ptm <- proc.time()
#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")
#testing if docker is running
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 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)
}
tmp.folder <- gsub(":","-",gsub(" ","-",date()))
scrat_tmp.folder=file.path(scratch.folder, tmp.folder)
writeLines(scrat_tmp.folder,paste(data.folder,"/tempFolderID", sep=""))
cat("\ncreating a folder in scratch folder\n")
dir.create(file.path(scrat_tmp.folder))
### copying fastq files
dir <- dir(data.folder)
dir <- dir[grep(".fasta.gz$", dir)]
cat("\ncopying \n")
if(length(dir)==0){
cat(paste("It seems that in ", data.folder, "there are not fasta files"))
system("echo 1 >& ExitStatusFile")
setwd(home)
return(1)
}else if(length(dir)>1){
cat(paste("It seems that in ", data.folder, "there is more than 1 fasta files"))
system("echo 2 >& ExitStatusFile")
setwd(home)
return(2)
}else{
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
system(paste("cp ",data.folder,"/",dir, " ",scratch.folder,"/",tmp.folder,"/",dir, sep=""))
system(paste("chmod 777 -R", file.path(scratch.folder, tmp.folder)))
}
###
#executing the docker job
params <- paste("--cidfile ",data.folder,"/dockerID -v ",scrat_tmp.folder,":/scratch -v ", data.folder, ":/data -d docker.io/repbioinfo/cdhit.2019.01:cdhit-V4.8.1 bash /bin/trim.sh ", dir, " ", min.length, sep="")
resultRun <- runDocker(group=group, params=params)
#waiting for the end of the container work
if(resultRun==0){
cat("\nTrimming 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("trimFasta user run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("trimFasta system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("trimFasta elapsed run time mins ",ptm[3]/60, sep="")
writeLines(tmp.run,"run.info")
}else{
tmp.run <- NULL
tmp.run[1] <- paste("trimFasta run time mins ",ptm[1]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("trimFasta system run time mins ",ptm[2]/60, sep="")
tmp.run[length(tmp.run)+1] <- paste("trimFasta 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,"/", substr(container.id,1,12),"_trimFasta.log", sep=""))
system(paste("docker rm ", container.id, sep=""))
#removing temporary folder
cat("\n\nRemoving the temporary file ....\n")
system(paste("rm -R ",scrat_tmp.folder))
system("rm -fR out.info")
system("rm -fR dockerID")
system("rm -fR tempFolderID")
system(paste("cp ",paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
setwd(home)
}
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