comparison add_expression_HPA.R @ 12:dbeabf9bf091 draft

planemo upload commit 51fc514a85c1055cab5bb6e76c90f3da7e648101-dirty

11:e109cacd75b2

    return (TRUE)
  }else if (any(is.element(c("f","false"),tolower(x)))){
    return (FALSE)
  }else{
    return(NULL)
  }
}

add_expression = function(input, atlas, options) {
  input <- unique(input[!is.na(input)])

    colnames(res)=colnames(tab)
  }
  return(res)
}

main = function() {
  args <- commandArgs(TRUE)
  if(length(args)<1) {
    args <- c("--help")
  }
  

  # Parse arguments
  parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
  argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
  args <- as.list(as.character(argsDF$V2))
  names(args) <- argsDF$V1

  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
  #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
  
  inputtype = args$inputtype
  if (inputtype == "copypaste") {
    input = strsplit(args$input, "[ \t\n]+")[[1]]
  } else if (inputtype == "tabfile") {
    filename = args$input
    ncol = args$column
    # Check ncol
    if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {

    } else {
      ncol = as.numeric(gsub("c", "", ncol))
    }
    header = str2bool(args$header)
    file = read_file(filename, header)
    file = one_id_one_line(file,ncol)
    input = unlist(sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
    input = input[which(!is.na(input))]
  }

  # Read protein atlas
  protein_atlas = args$atlas
  protein_atlas = read_file(protein_atlas, T)

  # Add expression
  output = args$output
  options = strsplit(args$select, ",")[[1]]
  res = add_expression(input, protein_atlas, options)
  
  # Write output
  if (is.null(res)) {
    write.table("None of the input ENSG ids are can be found in HPA data file",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
  } else {
    if (inputtype == "copypaste") {
      input <- data.frame(input)
      output_content = merge(input,res,by.x=1,by.y="row.names",incomparables = NA, all.x=T)
      colnames(output_content)[1] = "Ensembl"
    } else if (inputtype == "tabfile") {
      output_content = merge(file, res, by.x=ncol, by.y="row.names", incomparables = NA, all.x=T)
      output_content = order_columns(output_content,ncol)
    }

12:dbeabf9bf091

    return (TRUE)
  }else if (any(is.element(c("f","false"),tolower(x)))){
    return (FALSE)
  }else{
    return(NULL)
  }
}

stopQuietly <- function(...) {
  blankMsg <- sprintf("\r%s\r", paste(rep(" ", getOption("width")-1L), collapse=" "));
  stop(simpleError(blankMsg));
} # stopQuietly()

check_ensembl_geneids <- function(vector,type) {
  ensembl_geneid_pattern = "^ENS[A-Z]+[0-9]{11}$|^[A-Z]{3}[0-9]{3}[A-Za-z](-[A-Za-z])?$|^CG[0-9]+$|^[A-Z0-9]+[.][0-9]+$|^YM[A-Z][0-9]{3}[a-z][0-9]$"
  res = grepl(ensembl_geneid_pattern,vector)
  if (all(!res)){
    cat("No Ensembl geneIDs found in entered ids")
    stopQuietly()
  } else if (any(!res)) {
    cat(paste(sep="",collapse = " ",c(sum(!res, na.rm=TRUE),'IDs are not ENSG IDs, please check:\n')))
    not_geneids <- sapply(vector[which(!res)], function(x) paste(sep="",collapse = "",x,"\n"),USE.NAMES = F)
    cat(not_geneids)
  }
}

add_expression = function(input, atlas, options) {
  input <- unique(input[!is.na(input)])

    colnames(res)=colnames(tab)
  }
  return(res)
}

get_args <- function(){
  args <- commandArgs(TRUE)
  if(length(args)<1) {
    args <- c("--help")
  }
  

  # Parse arguments
  parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
  argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
  args <- as.list(as.character(argsDF$V2))
  names(args) <- argsDF$V1
  
  return(args)
}

is_col_in_file <- function(file,ncol) { 
  is_in_file = (ncol <= ncol(file) && ncol > 0)
  if (!is_in_file){
    cat(paste(sep = "", collapse = " ", c("Column",ncol,"not found in file") ))
    stopQuietly()
  }
}

main = function() {
  
  args = get_args()

  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
  #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
  
  inputtype = args$inputtype
  if (inputtype == "copypaste") {
    ids = strsplit(args$input, "[ \t\n]+")[[1]]
  } else if (inputtype == "tabfile") {
    filename = args$input
    ncol = args$column
    # Check ncol
    if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {

    } else {
      ncol = as.numeric(gsub("c", "", ncol))
    }
    header = str2bool(args$header)
    file = read_file(filename, header)
    is_col_in_file(file,ncol)
    file = one_id_one_line(file,ncol)
    ids = unlist(sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
    ids = ids[which(!is.na(ids))]
  }
  check_ensembl_geneids(ids)

  # Read protein atlas
  protein_atlas = args$atlas
  protein_atlas = read_file(protein_atlas, T)

  # Add expression
  output = args$output
  options = strsplit(args$select, ",")[[1]]
  res = add_expression(ids, protein_atlas, options)
  
  # Write output
  if (is.null(res)) {
    write.table("None of the ENSG ids entered can be found in HPA data file",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
  } else {
    if (inputtype == "copypaste") {
      ids <- data.frame(ids)
      output_content = merge(ids,res,by.x=1,by.y="row.names",incomparables = NA, all.x=T)
      colnames(output_content)[1] = "Ensembl"
    } else if (inputtype == "tabfile") {
      output_content = merge(file, res, by.x=ncol, by.y="row.names", incomparables = NA, all.x=T)
      output_content = order_columns(output_content,ncol)
    }