R/newDir.R

In batman: Bayesian AuTomated Metabolite Analyser for NMR spectra

newDir<-function(runBATMANDir = getwd(), overwriteFile = FALSE)
{
  ## written by Dr. Jie Hao, Imperial College London
  ## create a new directory with installed data files
  dirRoot<-paste(runBATMANDir,"/runBATMAN",sep="")
  if(!file.exists(dirRoot)) {
    dir.create(dirRoot)
  }
  dirIP<-paste(dirRoot,"/BatmanInput",sep="")
  if(!file.exists(dirIP)){
    dir.create(dirIP)
  }
  dirPST<-paste(dirIP,"/PureSpectraTemplate",sep="")
  if(!file.exists(dirPST)){
    dir.create(dirPST)
  }
  extdir<-system.file("extdata",package="batman")
  
  dirRastGln<-paste(extdir,"/PureSpectraTemplate/L-Glutamine.txt",sep="")
  cp<-file.copy(dirRastGln,dirPST,overwrite=overwriteFile)
  
  ## dirTPure<-paste(dirIP,"/testBrukerPureSpecForRasterTemplate",sep="")
  ##  if(!file.exists(dirTPure)){
	##  	dir.create(dirTPure)
	## }
  
  ## dirTPure1<-paste(dirTPure,"/testPure1",sep="")
  ## if(!file.exists(dirTPure1)){
  ##   dir.create(dirTPure1)
  ## }

  dirOP<-paste(dirRoot,"/BatmanOutput",sep="")
  if(!file.exists(dirOP)) {
    dir.create(dirOP)
  }

	
	## src.dir <- paste(extdir,"/testBrukerPureSpecForRasterTemplate/testPure1",sep="")
	## dest.dir <-dirTPure1
	
	## file.names <- dir(src.dir)
	## sapply(file.names, function(x) {
	## 	   file.copy(from=paste(src.dir, x, sep="/"),
	## 				 to=paste(dest.dir, x, sep="/"),
	##				 overwrite = FALSE) })
	
	
  dirbo<-paste(extdir,"/batmanOptions.txt",sep="")
  cp<-file.copy(dirbo,dirIP, overwrite=overwriteFile)
  dird<-paste(extdir,"/NMRdata.txt",sep="")
  cp<-file.copy(dird,dirIP, overwrite=overwriteFile)
  dirL<-paste(extdir,"/metabolitesList.csv",sep="")
  cp<-file.copy(dirL,dirIP, overwrite=overwriteFile)
  dirR<-paste(extdir,"/multi_data.csv",sep="")
  cp<-file.copy(dirR,dirIP,overwrite=overwriteFile)
  dirRU<-paste(extdir,"/multi_data_user.csv",sep="")
  cp<-file.copy(dirRU,dirIP,overwrite=overwriteFile)
  
  dirRU_adj<-paste(extdir,"/multi_data_user_adj.csv",sep="")
  cp<-file.copy(dirRU_adj,dirIP,overwrite=overwriteFile)
  
  dirA<-c(dirRoot, dirIP, dirOP, dirPST)
  return (dirA)
}