R/createAromaArchitecture.R

In MPAgenomics: Multi-Patient Analysis of Genomic Markers

#' Create the architecture required by aroma packages
#' 
#' @title Create aroma architecture
#' @param dataSetName name of the data set
#' @param chipType type of the chip used for obtaining the data 
#' @param path path where folders are created
#' @param verbose if TRUE, print details of the process
#' @return No return value, called for side effects.
#'
#' @author Quentin Grimonprez
#'
#' @details This function creates the following architecture:
#'Architecture to create:
#'   <path>
#'     +- annotationData/
#'     |  +- chipTypes/
#'     |     +- <chipType>/ <-- must match exactly the name of the CDF file (fullname minus tags)
#'     |        +- CDF file(s) and other annotation (possibly subdirectories)
#'     |
#'     +- rawData/
#'        +- <dataSetName>/
#'           +- <chipType>/ <-- must match exactly a chip type folder under annotationData/
#'              +- CEL files
#'
#'
createEmptyArchitecture=function(dataSetName,chipType,path=".",verbose=TRUE)
{
  #check arguments
  if(missing(dataSetName))
    stop("dataSetName is missing.")
  if(missing(chipType))
    stop("chipType is missing.")
  if(!is.character(dataSetName))
    stop("dataSetName must be a string.")
  if(!is.character(chipType))
    stop("chipType must be a string.")
  
  #create rawData
  if(!file.exists(paste0(path,"/rawData/",dataSetName,"/",chipType)))
  {
    dir.create(paste0(path,"/rawData/",dataSetName,"/",chipType),recursive=TRUE)
    ok1=file.access(paste0(path,"/rawData/",dataSetName,"/",chipType), mode = 0)
    if(ok1 != 0)
      stop(paste0("Can not create \"",path,"/rawData/",dataSetName,"/",chipType,"\" folder."))
    else
    {
      if(verbose)
        message(gsub("//","/",paste0("Folder \"",path,"/rawData/",dataSetName,"/",chipType,"\" created.")),"\n")
    }
  }
  else
    message("The folder",paste0(path,"/rawData/",dataSetName,"/",chipType),"already exits.")
  
  #create annotationData
  if(!file.exists(paste0(path,"/annotationData/chipTypes/",chipType)))
  {
    dir.create(paste0(path,"/annotationData/chipTypes/",chipType),recursive=TRUE)
    
    #test existence of the created folders
    ok2=file.access(paste0(path,"/annotationData/chipTypes/",chipType), mode = 0)

    if(ok2 != 0)
      stop(paste0("Can not create \"",path,"/annotationData/chipTypes/",chipType,"\" folder."))  
    else
    {
      if(verbose)
        message(gsub("//","/",paste0("Folder \"",path,"/annotationData/chipTypes/",chipType,"\" created.")),"\n")
    }
  }
  else
    message("The folder",paste0(path,"/annotationData/chipTypes/",chipType),"already exits.")
  
  return(invisible(TRUE))
}

# @title Copy data files in the appropriate folder
# @param dataSetName Name of the data set
# @param dataSetPath Path where the data files can be found
# @param chipName Type of the chip used for the data 
# @param path Path where the rawData folder can be found
# @param verbose if TRUE, print details of the process
# @return No return value, called for side effects.
#
# @author Quentin Grimonprez

#@note WARNING : Files are copied, not moved. 
copyDataFiles=function(dataSetName,dataSetPath,chipName,path,verbose)
{
  if(verbose)
    message("\nCopy data files:\n")
  
  #list all the files in the dataSet
  fileNames=list.files(dataSetPath)
  
  lapply(fileNames,FUN=function(fileName)
    {
      #check the extension
      if(toupper(substr(fileName,nchar(fileName)-3,nchar(fileName)))==".CEL")
      {
        #copy the file in rawData/<dataSetName>/<chipName>/
        if(file.exists(paste0(path,"/rawData/",dataSetName,"/",chipName,"/",fileName)))
        {
          if(verbose)
            message("File",fileName," already exists.\n")
        }
        else
        {
          if(verbose)
            message(paste0("Copying ",fileName,"..."))
          file.copy(paste0(dataSetPath,"/",fileName),paste0(path,"/rawData/",dataSetName,"/",chipName,"/",fileName),overwrite=FALSE)
          if(verbose)
            message("\t DONE.\n")
        }

      }
    }
  )#end lapply
  
  return(invisible(TRUE)) 
}

# @title Copy chip files in the appropriate folder
# @param pathToChipFiles path where to find the chip files
# @param chipName type of the chip used for the data 
# @param path path where to find rawData folder
# @param verbose if TRUE, print details of the process
# @return No return value, called for side effects.
#
#@note WARNING : Files are copied, not moved.  Overwrite existing files with the same name.
# All the chip files have the form : chipName,Tags.extension.
# Extension can be ugp, ufl, cdf or acs
#
# @author Quentin Grimonprez
#
copyChipFiles=function(pathToChipFiles,chipName,path,verbose)
{
  if(verbose)
    message("\nCopy chip files:\n")
  
  #valid extensions for chip files
  validExtension=c(".ugp",".ufl",".cdf",".acs")
  
  #list all the files in the dataSet
  fileNames=list.files(pathToChipFiles)
    
  lengthChipName=nchar(chipName)
  
  successCopy=lapply(fileNames,FUN=function(fileName)
  {
    #check the extension
    if(tolower(substr(fileName,nchar(fileName)-3,nchar(fileName)))%in%validExtension)
    { 
      #check if it is a file for the good chip
      if(chipName==substr(fileName,1,nchar(chipName)))
      {
        #copy the file in annotationData/<chipType>/
        if(verbose)
          message(paste0("Copying ",fileName,"..."))
        file.copy(paste0(pathToChipFiles,"/",fileName),paste0(path,"/annotationData/chipTypes/",chipName,"/",fileName),overwrite=TRUE)
        
        #change ".Full" in ",Full" in cdf files
        if(substr(fileName,nchar(fileName)-8,nchar(fileName)-4)==".Full")
        {
          newfileName=paste0(substr(fileName,1,nchar(fileName)-9),",Full",substr(fileName,nchar(fileName)-3,nchar(fileName)))
          renameFile(paste0(path,"/annotationData/chipTypes/",chipName,"/",fileName),paste0(path,"/annotationData/chipTypes/",chipName,"/",newfileName))          
        }
        
        if(verbose)
          message("\t DONE.\n")
        return(TRUE)
      }
      else
      {
        if(verbose)
          message("File name: ",fileName,"doesn't correspond with specified chip name :",chipName ,"\n")
        return(FALSE)
      }
    }
    else
    {
      return(FALSE)
    }
    
  }
  )#end lapply
  
  if(sum(unlist(successCopy))==0)
    message("No chip files copied.")
  
  return(invisible(TRUE))   
}

#check if the chipfiles are good
#@author Quentin Grimonprez
.checkChipType=function(chipType,tag)
{
  allpkg=TRUE
  if(!suppressPackageStartupMessages(requireNamespace("aroma.affymetrix", quietly=TRUE) ) )
  {
    message("Package not found: aroma.affymetrix. For download it:\n")
    message("source(\"http://callr.org/install#HenrikBengtsson/sfit\")\n")
    message("if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n")
    message("install.packages(\"BiocManager\")\n")
    message("BiocManager::install(\"affxparser\")\n")
    message("BiocManager::install(\"DNAcopy\")\n")
    message("BiocManager::install(\"aroma.light\")\n")
    message("install.packages(\"aroma.affymetrix\")\n")
    allpkg=FALSE
  }
  
  if(!allpkg)
    stop("You have to install some packages : Follow the printed informations.")
  
  requireNamespace("aroma.core")
  
  result <- try(cdf <- aroma.affymetrix::AffymetrixCdfFile$byChipType(chipType, tags=tag),silent=TRUE)
  if(class(result)[1]=="try-error")
  {
    stop(geterrmessage())
    #stop(paste0("Problem with cdf files for the chip ",chipType," with tag ",tag))
  }

  #check if ugp or ufl files with the specified tags exist
  file=list.files(paste0("annotationData/chipTypes/",chipType))
  if(!is.null(tag))
  {
    tagfile=file[grep(tag,file)]
    
    tagfile=tolower(tagfile)
    ugpfile=tagfile[grep(".ugp",tagfile)]
    uflfile=tagfile[grep(".ufl",tagfile)]
    
    if(length(ugpfile)==0)
      stop(paste0("No ugp files with tag ",tag))
    if(length(uflfile)==0)
      stop(paste0("No ufl files with tag ",tag))
  }
    
  result <- try(gi <- aroma.affymetrix::getGenomeInformation(cdf),silent=TRUE)
  if(class(result)[1]=="try-error")
  {
    stop(geterrmessage())
    #stop(paste0("No ugp files for the chip ",chipType," with tag ",tag))
  }

  result <- try(si <- aroma.affymetrix::getSnpInformation(cdf),silent=TRUE)
  if(class(result)[1]=="try-error")
  {
    stop(geterrmessage())
    #stop(paste0("No ufl files for the chip ",chipType," with tag ",tag))
  }

  result <- try(acs <- aroma.core::AromaCellSequenceFile$byChipType(aroma.core::getChipType(cdf, fullname=FALSE)),silent=TRUE)
  if(class(result)[1]=="try-error")
  {
    stop(geterrmessage())
    #stop(paste0("No acs files for the chip ",chipType," with tag ",tag))
  }

  
 return(invisible(TRUE))
}


#' Create the architecture required by aroma.* packages and copy files into created folders.
#' 
#' @title Create aroma architecture and copy files
#' 
#' @param dataSetName The name of the data-set folder to create
#' @param chipType The name of the used chip 
#' @param dataSetPath Path to the folder containing the data CEL files
#' @param chipFilesPath Path to the folder containing the chip files
#' @param path Path where the architecture should be created (default=".")
#' @param verbose Print information during the process (default=FALSE)
#' @param tags Common tag which appears in the different file names (cdf, ugp, ufl) of the chip. For no tag, use tags=NULL (default = NULL). See details for more information.
#' @return No return value, called for side effects.
#' @seealso copyChipFiles, copyDataFiles, createAromaArchitecture
#' 
#' @details
#' All the cdf chip file names must follow the following rule : <chipType>,<Tags>.cdf
#' 
#' Multiples tags must be separated by a comma. If there is no tag, the pattern is <chipType>.cdf
#' 
#' @examples
#' \dontrun{
#' #DO NOT EXECUTE before reading the vignette
#'   createArchitecture("test1","GenomeWideSNP_6","./celPATH","./chipPATH",path=".",TRUE,"Full")
#' }
#' 
#' @author Quentin Grimonprez
#' 
#' @export
createArchitecture=function(dataSetName,chipType,dataSetPath,chipFilesPath,path=".",verbose=FALSE, tags=NULL)
{
  if(!suppressPackageStartupMessages(requireNamespace("aroma.affymetrix", quietly=TRUE) ) )
  {
    message("Package not found: aroma.affymetrix. For download it:\n")
    message("source(\"http://callr.org/install#HenrikBengtsson/sfit\")\n")
    message("if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n")
    message("install.packages(\"BiocManager\")\n")
    message("BiocManager::install(\"affxparser\")\n")
    message("BiocManager::install(\"DNAcopy\")\n")
    message("BiocManager::install(\"aroma.light\")\n")
    message("install.packages(\"aroma.affymetrix\")\n")
    allpkg=FALSE
  }
#   else
#     message("Package aroma.affymetrix loaded.\n")
  
   createEmptyArchitecture(dataSetName,chipType,path,verbose)
   copyChipFiles(chipFilesPath,chipType,path,verbose)
  .checkChipType(chipType,tags)
   copyDataFiles(dataSetName,dataSetPath,chipType,path,verbose)

  
  return(invisible(TRUE))  
}