R/platypusFilter.R

Defines functions platypusFilter

Documented in platypusFilter

#' @title Platypus filter analysis NOT READY TO GO ON STABLE to be used in case the full platypus workflow fail.
#' @description This function executes platypusFilter filtering the single_variants.vcf generated by platypys function.
#' @param group, a character string. Two options: sudo or docker, depending to which group the user belongs
#' @param data.folder, a character string indicating the folder where bams and vcf files are located and where output will be written
#' @param scratch.folder, a character string indicating the path of the scratch folder
#' @param GQ, min GQ value to consider (extreme included)
#' @param minSampGQ, min number of samples with GQ value (extreme included), usually we start with 85\% of the samples
#' @param NR, min NR value to consider (extreme included), the number of reads covering the SNV region
#' @param minSampNR, min number of samples with NR value (extreme included), usually we start with 85\% of the samples
#' @param NV, min NV value to consider (extreme included), the n of reads with the SNV
#' @param minSampNV, min number of samples with NV value (extreme included)
#' @param normal_samples, string with names (group names of bam files) of normal samples separated by hash, write NULL if you do not want to use GT filter in normal samples
#' @param GT_normal, GT value in normal samples to consider, type "NO" if you do not want to use this filter, else e.g. you might use 0/0
#' @param minSampGT_normal, min number of normal samples with GT value
#' @param tumoral_samples, string with names (group names of bam files) of tumoral samples separated by &, write NULL if you do not want to use GT filter in normal samples
#' @param GT_tumoral, GT value in tumoral samples to consider, type "NO" if you do not want to use this filter. Type e.g. 0/0 if you do not want to consider this genotype.
#' @param minSampGT_tumoral, min number of tumoral samples in which the GT value is NOT present
#' @param stringent_filter, To enable the filter (it keeps only the variants with "PASS" value or the variants that have only the "alleleBias" value) use 1 or 0 to disable it
#' @param annotation, hg19 and mm10 are actually available for the annotation of the detected SNVs
#' @author Riccardo Panero, riccardo.panero[at]gmail[dot]com, Bioinformatics and Genomics unit, University of Torino Italy
 
#' @examples
#' \dontrun{
#'     #filtering platypus results 
#'  platypusFilter(group="docker", data.folder="/archive/home/rcaloger/data/platypus_tests/mm10ENSEMBL", 
#'         scratch.folder="/scratch/users/rcaloger/",
#'         GQ=10, minSampGQ=2, NR=10, minSampNR=2, NV=3, 
#'         minSampNV=1, normal_samples="MAMBO43", GT_normal="0/0", 
#'         minSampGT_normal=1, tumoral_samples="MAMBO43TRT#MAMBO43TRNT", GT_tumoral="0/0", 
#'         minSampGT_tumoral=1, stringent_filter=0, annotation="mm10")

#' }

#' @export

platypusFilter <- function(group=c("sudo","docker"), data.folder=getwd(), scratch.folder, GQ, minSampGQ, NR, minSampNR, NV, minSampNV, 
                     normal_samples, GT_normal, minSampGT_normal, tumoral_samples, GT_tumoral, minSampGT_tumoral, stringent_filter, annotation){
  
  #running time 1
  ptm <- proc.time()
  #running time 1

  
  #storing the position of the home folder  
  home <- getwd()
  #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)
  }
  #creating a tmp folder in scratch
  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))
  if(length(dir(data.folder)[grep("run.info",dir(data.folder))]) == 0){
    system(paste("touch ", scrat_tmp.folder,"/run.info",sep=""))
  }else{
    system(paste("mv run.info ", scrat_tmp.folder,sep=""))
  }
  
  #getting in the tmp folder in scratch folder
  setwd(data.folder)
  
  system("echo 0 > ExitStatusFile 2>&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)
  }


  #executing the docker job

params <- paste("--cidfile ",data.folder,"/dockerID -v ", data.folder,":/data -v ", scrat_tmp.folder, ":/data/scratch -d docker.io/repbioinfo/platypus.2017.01 Rscript /bin/platypus_filter_annotation_split.R ", GQ, " ", minSampGQ, " ", NR, " ", minSampNR, " ", NV, " ", minSampNV, " ", 
                normal_samples, " ", GT_normal, " ", minSampGT_normal, " ", tumoral_samples, " ", GT_tumoral, " ", minSampGT_tumoral, " ", stringent_filter, " ", annotation, sep="")
    resultRun <- runDocker(group=group, params=params)
 
    #waiting for the end of the container work
    if(resultRun==0){
      cat("\n Platypus filter analysis  is finished\n")
    }    
     
      setwd(scrat_tmp.folder)
      cat("\n\nRemoving the temporary file ....\n")
      system(paste("cp ",paste(path.package(package="docker4seq"),"containers/containers.txt",sep="/")," ",data.folder, sep=""))
      system(paste("mv *platypus_filtered_annotated.txt ", data.folder, sep = ""))


      setwd(data.folder)
      #running time 2
      ptm <- proc.time() - ptm
      dir <- dir(scratch.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("split platypus filter user run time mins ",ptm[1]/60, sep="")
        tmp.run[length(tmp.run)+1] <- paste("split platypus filter system run time mins ",ptm[2]/60, sep="")
        tmp.run[length(tmp.run)+1] <- paste("split platypus filter elapsed run time mins ",ptm[3]/60, sep="")
        writeLines(tmp.run,"run.info")
      }else{
        tmp.run <- NULL
        tmp.run[1] <- paste("split platypus filter run time mins ",ptm[1]/60, sep="")
        tmp.run[length(tmp.run)+1] <- paste("split platypus filter system run time mins ",ptm[2]/60, sep="")
        tmp.run[length(tmp.run)+1] <- paste("split platypus filter elapsed run time mins ",ptm[3]/60, sep="")
        writeLines(tmp.run,"run.info")
      }
  
      container.id <- readLines(paste(data.folder,"/dockerID", sep=""), warn = FALSE)
      system(paste("docker logs ", substr(container.id,1,12), " &> ", "platypusFilter_",substr(container.id,1,12),".log", sep=""))
 #     system(paste("docker rm ", container.id, sep=""))
      system("rm -fR dockerID")
      system("rm  -fR tempFolderID")
      setwd(home)
      
}
  
kendomaniac/docker4seq documentation built on Oct. 16, 2023, 2:30 a.m.