R/RMiXCR_reports.R

In elmerfer/RMiXCR: An easy wrapper for MiXCR software

#' Report
#' @description 
#' In order to export alignment results or clones from a binary file (.clns) to a human-readable tab or excel file
#' @details 
#' The resulting tab-delimited text file or excel file (type param) will contain columns with different types of information. 
#' If no options are specified (otherFields), the default set of columns - which is sufficient in most cases - will be exported. 
#' The possible columns include. See details in [MiXCR main page](https://mixcr.readthedocs.io/en/master/export.html): 
#' aligned sequences, qualities, all or just best hit for V, D, J and C genes, corresponding alignments, nucleotide and amino acid sequences of gene region present in sequence, etc. When exporting clones, the additional columns include: clone count, clone fraction etc.
#' One can customize the list of fields that will be exported by passing parameters to export commands (not implemented yet). 
#' @usage 
#' Report(clonsFile, type = c("full","min"), otherFields, fileType = c("Excel","tab"))
#' @param clonsFile the full path to the clone file (subjsect.R1.fastq.clones.clns) as returned by \code{\link{RunMiXCRseqClones}}
#' @param type string "full" (default) or "min"
#' @param otherFields other fields (not implemented yet)
#' @param fileType Excel or tab (tab delimited)
#' @export

Report <- function(clonsFile, type = c("full","min"), otherFields, fileType = c("Excel","tab")){
  software <- RMiXCR:::.OpenConfigFile()
  cat(paste0("\nExporting clones to Excel file"))
  # java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.clones.txt
  clonsFile <- clonsFile[stringr::str_detect(clonsFile,".clones.clns")]
  if(length(clonsFile)<1){
    stop("ERROR, clones.clns file not found")
  }
  type <- match.arg(type[1], c("full","min"))
  fileType <- match.arg(toupper(fileType[1]) , toupper(c("Excel","tab")))
  assemble.ofile <- clonsFile
  out.tab.file <- stringr::str_replace(assemble.ofile,".clns",paste0("_",type,".tab"))
  st <- system2(command = "java",
                args = c(software$mixcr$base.args,
                         "exportClones", 
                         paste0("--preset ", type),
                         assemble.ofile, 
                         out.tab.file), 
                stderr = TRUE )
  if(file.exists(out.tab.file)==FALSE){
    stop("Fail in create clones file")
  }
  if(fileType == "TAB") return(out.tab.file)
  tab.file <- read.table(out.tab.file,h=T, sep="\t")
  openxlsx::write.xlsx(tab.file, file = stringr::str_replace(out.tab.file,".tab",".xlsx"))
  if(file.exists(stringr::str_replace(out.tab.file,".tab",".xlsx"))){
    file.remove(out.tab.file)
  }else{
    cat(paste0("\nExcel file failed"))
  }
  return(stringr::str_replace(out.tab.file,".tab",".xlsx"))
}


#' RunMiXCRexportExcel
#' @param clonsFile (string) the clone file. No IG clones
#' @export
#' 
RunMiXCRexportExcel <- function(clonsFile ){
  software <- RMiXCR:::.OpenConfigFile()
  cat(paste0("\nExporting clones to Excel file"))
  # java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.clones.txt
  clonsFile <- clonsFile[stringr::str_detect(clonsFile,".clones.clns")]
  if(length(clonsFile)<1){
    stop("ERROR, clones.clns file not found")
  }
  if(file.exists(clonsFile)){
    assemble.ofile <- clonsFile
    st <- system2(command = "java",
                  args = c(software$mixcr$base.args,
                           "exportClones", "--chains TCR",
                           assemble.ofile, 
                           stringr::str_replace(assemble.ofile,".clns",".tab")
                  ), stderr = TRUE )
    if(any(stringr::str_detect(st, "ERROR"))){
      cat("\nSomething HAPPEND on clns")
    }
    # java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones --chains TCR -p min ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.vmin.clones.txt
    
    st <- system2(command = "java",
                  args = c(software$mixcr$base.args,
                           "exportClones", "--chains TCR",
                           "-p min",
                           assemble.ofile, 
                           stringr::str_replace(assemble.ofile,".clns",".vmin.tab")
                  ),  stderr = TRUE)
    if(any(stringr::str_detect(st, "ERROR"))){
      cat("\nSomething HAPPEND on vmin")
    }
    gen.files <- stringr::str_replace(assemble.ofile,".clns",".vmin.tab")
    # java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.vdetails.clones.txt
    system2(command = "java",
            args = c(software$mixcr$base.args,
                     "exportClones", "-count",
                     "-vhit", "-dhit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
                     "-nFeature CDR3", "-aaFeature CDR3",
                     assemble.ofile, 
                     stringr::str_replace(assemble.ofile,".clns",".vdetails.clones.tab")
            ), stderr = TRUE)
    gen.files <- c(gen.files,stringr::str_replace(assemble.ofile,".clns",".vdetails.clones.tab"))
    # java -jar -Xmx6g $MIXCR_BIN_DIR/mixcr.jar exportClones -count -vHit -dHit -jHit -cHit -vHits -dHits -jHits -cHits -nFeature CDR3 -c TRA -aaFeature CDR3 ${OUTPUT_FILE}.clones.clns ${OUTPUT_FILE}.TRA.clones.txt
    chains <- c("IGH","IGK","TRA","TRB","TRD","TRG")
    gen.files <- c(gen.files,unlist(lapply(chains, function(ch){
      sys.out <- system2(command = "java",
                         args = c(software$mixcr$base.args,
                                  "exportClones", "-count",
                                  "-vHit", "-dHit", "-jHit", "-cHit", "-vHits", "-dHits", "-jHits", "-cHits",
                                  "-nFeature CDR3", paste0("-c ",ch), "-aaFeature CDR3",
                                  assemble.ofile, 
                                  stringr::str_replace(assemble.ofile,".clns",paste0(".",ch,".clones.tab"))
                         ),stderr = TRUE)
      ret.val <- stringr::str_replace(assemble.ofile,".clns",paste0(".",ch,".clones.tab"))
      
      attr(ret.val,"status") <- attr(sys.out,"status")
      attr(ret.val,"errmsg") <- attr(sys.out,"errmsg")
      return(ret.val)
    })))
    
    
    gen.files <- gen.files[file.exists(gen.files)]
    to.excel <- lapply(gen.files, function(x){
      return(read.table(x,h=T, sep="\t"))  
    })
    aux.files.subfix <- c(".tab","vmin.tab",".vdetails.clones.tab",".TRA.clones.tab",".TRB.clones.tab",".TRG.clones.tab",".TRD.clones.tab")
    names(to.excel) <- c(stringr::str_remove(c("clones.tab","vmin.tab","vdetails.clones.tab","TRA.clones.tab","TRB.clones.tab","TRG.clones.tab","TRD.clones.tab"),".tab")
    openxlsx::write.xlsx(to.excel, stringr::str_replace(assemble.ofile,".clns",".xlsx"))
    file.remove(c(gen.files,stringr::str_replace(assemble.ofile,".clns",".tab")))
    if(file.exists(stringr::str_replace(assemble.ofile,".clns",".xlsx"))){
      message(paste0("\nFile saved as :",stringr::str_replace(assemble.ofile,".clns",".xlsx")))
      return(invisible(aux.files.subfix))          
    }
    return(NA)
    
  }else{
    message(paste0("\nFile not found :",clonsFile))
    return(NA)
  }
  
}