R/callQoRT.R

In aiminy/PathwaySJ: A R package for GO term enrichment analysis with the flexible bias factor adjustment

#' @ Use QoRTs to get the count of subfeatures in each gene
#'
#' @ cmd1
#' @ inputfile:bam file, gene annotation file,
#' @ outfile
#'
#' @return
#' @export
#'
#' @examples
#'
#' dir.name="/media/H_driver/Aimin_project/GOSJ_example_data/"
#' dir.name="/media/H_driver/Aimin_project/GOSJ_STAR_Bam/"
#'
#' file.name=dir(dir.name,recursive = TRUE,pattern="sorted.bam")
#' file.name.whole<-paste0(dir.name,file.name)
#' file.name.selected<-file.name.whole
#' file.name.selected.2<-as.list(file.name.selected)
#' names(file.name.selected.2)=sapply(strsplit(file.name.selected,split="\\/"),"[[",6)
#'
#' file.name.selected.3<-file.name.selected.2[-c(1,3)]
#'
#' cmd1="java -Xmx4000M -jar /home/aiminyan/QoRTs/QoRTsFullExampleData/QoRTsRelease/QoRTs.jar QC --noGzipOutput --keepMultiMapped"
#'
#' cmd2="java -Xmx5000M -jar /home/aiminyan/QoRTs/QoRTsFullExampleData/QoRTsRelease/QoRTs.jar QC --noGzipOutput"
#'
#' gtf1="/media/H_driver/Aimin_project/GTF_Files/Homo_sapiens.GRCh38.84.processed.sorted.2.gtf"
#'
#' re.out<-lapply(file.name.selected.3,callQoRT,gtf_file=gtf1,runing_cmd=cmd2)
#'

callQoRT<-function(input_file,runing_cmd,gtf_file){

  inputfile=paste(input_file,gtf_file,sep=" ")

  outfile=paste("",sapply(strsplit(input_file,split="\\/"),"[[",2),sapply(strsplit(input_file,split="\\/"),"[[",3),
                sapply(strsplit(input_file,split="\\/"),"[[",4),sapply(strsplit(input_file,split="\\/"),"[[",6),sep="/")


  cmd2=paste(runing_cmd,inputfile,outfile,sep=" ")

  print(cmd2)


  system(cmd2, intern = TRUE, ignore.stderr = TRUE)

  return(cmd2)

}