#' @title integrationPsblk
#' @description This function execute integrationPsblk analysis which search for correspondence between clusters of two different experiments using clusters-pseudo-bulks, z-scored on rows, and a subset of randomly selected genes. Thus, the function clustersBulk has to be run on the two datasets before their comparison.
#' @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 fileX, a character string indicating the path of the pseudobulkRow file, with file name and extension included.
#' @param fileY, a character string indicating the path of the pseudobulkRow file, with file name and extension included.
#' @param separatorX, separator used in count file, e.g. '\\t', ','
#' @param separatorY, separator used in count file, e.g. '\\t', ','
#' @param max.genes, MAX number of random genes to be used for each cluster, default 500
#' @param split.by, value indication the splitting range default 100. I.e. if max.genes= 500 with split.by set to 100 there will be 5 sets of genes selected 100, 200, 300, 400, 500
#' @param outputFolder, where results are placed
#' @author Luca Alessandri, alessandri [dot] luca1991 [at] gmail [dot] com, University of Torino
#'
#' @return A folder called XYpb with all the results generated. The final frequency table is saved in final_score.csv, which is made by the frequency of having Pearson >= 0.5 between X and Y datasets for each possible comparisons between the clusters of the X and Y experiment. Pearson correlation is calculated on 10000 random selections of genes for each threshold.
#' @examples
#' \dontrun{
#' library(rCASC)
#' integrationPsblk(group="docker",
#' scratch.folder="/scratch",
#' fileX="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX/CRC0327_NT_2_clx/VandE/VandE_bulkRow.csv",
#' fileY="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX/CRC0327_cetux_2_clx/VandE/VandE_bulkRow.csv",
#' separatorX=",",
#' separatorY=",",
#' max.genes=500,
#' split.by=100
#' outputFolder="/data/reanalysis_on_AIsc/comparing_CRC0327/NT_CTX"
#' )
#'}
#' @export
integrationPsblk <- function(group=c("sudo","docker"), scratch.folder, fileX, fileY, separatorX, separatorY, max.genes=500, split.by=100, outputFolder){
data.folder=outputFolder
#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))
#preprocess matrix and copying files
if(separatorX=="\t"){
separatorX="tab"
}
if(separatorY=="\t"){
separatorY="tab"
}
system(paste("cp ",fileX," ",scrat_tmp.folder,"/",sep=""))
fileX.file1 <- sapply(strsplit(basename(fileX), "\\."), function(x)x[1])
fileX.file2 <- sapply(strsplit(basename(fileX), "\\."), function(x)x[2])
fileX.file <- paste("X", fileX.file2, sep=".")
system(paste("mv ",scrat_tmp.folder,"/", basename(fileX)," ",scrat_tmp.folder,"/",fileX.file, sep=""))
system(paste("cp ",fileY," ",scrat_tmp.folder,"/",sep=""))
fileY.file1 <- sapply(strsplit(basename(fileY), "\\."), function(x)x[1])
fileY.file2 <- sapply(strsplit(basename(fileY), "\\."), function(x)x[2])
fileY.file <- paste("Y", fileY.file2, sep=".")
system(paste("mv ",scrat_tmp.folder,"/", basename(fileY)," ",scrat_tmp.folder,"/",fileY.file, sep=""))
fileX=paste("/scratch/",fileX.file,sep="")
fileY=paste("/scratch/",fileY.file,sep="")
#executing the docker job
params <- paste("--cidfile ",data.folder,"/dockerID -v ",scrat_tmp.folder,":/scratch -v ", data.folder, ":/data -d docker.io/repbioinfo/combinetoprnk Rscript /home/combineExperiments_toprnk.R ", max.genes, " ", fileX, " ", fileY," ", separatorX," ", separatorY, " ", split.by, sep="")
resultRun <- runDocker(group=group, params=params)
#waiting for the end of the container work
if(resultRun==0){
#system(paste("cp ", scrat_tmp.folder, "/*top* ", data.folder, sep=""))
}
#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("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,"run.info")
}else{
tmp.run <- NULL
tmp.run[1] <- paste("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,"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),".log", sep=""))
system(paste("docker rm ", container.id, sep=""))
#Copy result folder
cat("Copying Result Folder")
system(paste("cp -r ",scrat_tmp.folder,"/XYpb ",data.folder,"/",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="rCASC"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
setwd(home)
}
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