R/main.R

In Skhakmardan/MHiC: MHiC

main<-function(){
  cat("Tools for identify Hi-C significant interactions from different Hi-C data structure\nVersion : 1.0\n")

  cat("Please enter requirement parameters.\nyou can use MHiC function for Run this tool")

    reads_file<- readline(prompt="please enter read_pairs file path:")
    cat("\n")
    Digest_file<- readline(prompt="please enter Digest file path:")
    cat("\n")

    sample_name<- readline(prompt="please enter sample name:")
    cat("\n")
    cat("please select tools you worked")
    cat("\n")
    cat("1 : HiC_PRO \n2 : HiCUP \n3 : HOMER")
    tools_name<- readline(prompt="select:")
    if (tools_name == 1){
      tools_name<-"HiC_PRO"
    }
    else if (tools_name == 2){
      tools_name<-"HiCUP"
    }
    else if (tools_name == 3){
      tools_name<-"HOMER"
    }
    else{stop("please enter asked value.")}
    cat("\n")

    res<- readline(prompt="please enter bin size:")
    if(isNumeric(res)){
      res<-as.numeric(res)
    }
    else{rm(res)}
    cat("\n")
    cistrans<- readline(prompt="please select type of interactions [all/cis/trans]: ")
    cat("\n")

    parallel<- readline(prompt="do you need use this tool in parallel mode [y/n]:")
    if(as.character(parallel)=="y"){
      parallel<-TRUE
    cores<- readline(prompt="please enter cores number:")
    }
    else if(as.character(parallel)=="n"){parallel<-FALSE}
    else{ stop("this parameter value is [y/n]")}


    cat("\n")
    removeDiagonal<- readline(prompt="do you want remove Diagonal interaction [y/n]:")
    if(as.character(removeDiagonal)=="y"){removeDiagonal<- TRUE}
    else if(as.character(removeDiagonal)=="n"){removeDiagonal<- FALSE}

  result<-MHiC(as.character(reads_file),as.character(Digest_file)
               ,as.character(sample_name)
               ,as.character(tools_name),as.integer(res)
               ,as.character(cistrans)
               ,parallel, cores,removeDiagonal)


  return(result)

}