comparison id_converter_UniProt.R @ 5:0584344186eb draft

planemo upload commit 6e27a0eaf8172154128960497271e8f54341acd7-dirty

4:134949593a3b

#   Ensembl_ENSG: Ensembl gene identifiers (e.g. ENSG00000166913) 
#   Ensembl_ENST: Ensembl transcript identifiers (e.g. ENST00000353703; ENST00000372839)
#   Ensembl_ENSP: Ensembl protein identifiers (e.g. ENSP00000300161; ENSP00000361930)

mapping = function() {
  # Extract arguments
  args = commandArgs(trailingOnly = TRUE)
  #print(args)
  if (length(args) != 6) {
    stop("Not enough/Too many arguments", call. = FALSE)
  }
  else {
    input_id_type = args[1]
    list_id = args[2]
    list_id_input_type = args[3]
    options = strsplit(args[4], ",")[[1]]
    output = args[5]
    human_id_mapping_file = args[6]
    
    # Extract ID maps
    human_id_map = read.table(human_id_mapping_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "", quote = "")
    
    # Extract input IDs
    if (list_id_input_type == "list") {
      list_id = strsplit(args[2], " ")[[1]]
      # Remove isoform accession number (e.g. "-2")
      list_id = gsub("-.+", "", list_id)
    }
    else if (list_id_input_type == "file") {
      filename = as.character(strsplit(list_id, ",")[[1]][1])
      column_number = as.numeric(gsub("c", "" ,strsplit(list_id, ",")[[1]][2]))
      header = strsplit(list_id, ",")[[1]][3]
      file_all = readfile(filename, header)
      print(class(file_all))
      str(file_all)
      print(class(file_all[,1]))
      list_id = c()
      list_id = sapply(strsplit(file_all[,column_number], ";"), "[", 1)
      # Remove isoform accession number (e.g. "-2")
      list_id = gsub("-.+", "", list_id)
    }
    names = c()
    
    # Map IDs
    res = matrix(nrow=length(list_id), ncol=0)

    for (opt in options) {
      names = c(names, opt)
      mapped = human_id_map[match(list_id, human_id_map[input_id_type][,]),][opt][,]
      res = cbind(res, matrix(mapped))
    }
     
    # Write output
    if (list_id_input_type == "list") {
      res = cbind(as.matrix(list_id), res)
      names = c(input_id_type, names)
      colnames(res) = names
      write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE)
    }
    else if (list_id_input_type == "file") {
      names(res) = options
      names = c(names(file_all), names)
      output_content = cbind(file_all, res)
      colnames(output_content) = names
      write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
    }
  }
}

mapping()

5:0584344186eb

#   Ensembl_ENSG: Ensembl gene identifiers (e.g. ENSG00000166913) 
#   Ensembl_ENST: Ensembl transcript identifiers (e.g. ENST00000353703; ENST00000372839)
#   Ensembl_ENSP: Ensembl protein identifiers (e.g. ENSP00000300161; ENSP00000361930)

mapping = function() {
  args <- commandArgs(TRUE)
  if(length(args)<1) {
    args <- c("--help")
  }
  
  # Help section
  if("--help" %in% args) {
    cat("Selection and Annotation HPA
    Arguments:
        --ref_file: path to reference file (human_id_mapping_file.txt)
        --input_type: type of input (list of id or filename)
        --id_type: type of input IDs
        --input: list of IDs (text or filename)
        --column_number: the column number which contains list of input IDs
        --header: true/false if your file contains a header
        --target_ids: target IDs to map to 
        --output: output filename \n")
    q(save="no")
  }
  
  # 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

  input_id_type = args$id_type # Uniprot, ENSG....
  list_id_input_type = args$input_type # list or file
  options = strsplit(args$target_ids, ",")[[1]]
  output = args$output
  human_id_mapping_file = args$ref_file
    
  # Extract input IDs
  if (list_id_input_type == "list") {
    print(args$input)
    list_id = strsplit(args$input, "[ \t\n]+")[[1]]
    # Remove isoform accession number (e.g. "-2")
    list_id = gsub("-.+", "", list_id)
  }
  else if (list_id_input_type == "file") {
    filename = args$input
    column_number = as.numeric(gsub("c", "" ,args$column_number))
    header = args$header
    file_all = readfile(filename, header)
    list_id = c()
    list_id = sapply(strsplit(file_all[,column_number], ";"), "[", 1)
    # Remove isoform accession number (e.g. "-2")
    list_id = gsub("-.+", "", list_id)
  }

  # Extract ID maps
  human_id_map = read.table(human_id_mapping_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "", quote = "")
  
  names = c()
    
  # Map IDs
  res = matrix(nrow=length(list_id), ncol=0)

  for (opt in options) {
    names = c(names, opt)
    mapped = human_id_map[match(list_id, human_id_map[input_id_type][,]),][opt][,]
    res = cbind(res, matrix(mapped))
  }
     
  # Write output
  if (list_id_input_type == "list") {
    res = cbind(as.matrix(list_id), res)
    names = c(input_id_type, names)
    colnames(res) = names
    write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE)
  }
  else if (list_id_input_type == "file") {
    names(res) = options
    names = c(names(file_all), names)
    output_content = cbind(file_all, res)
    colnames(output_content) = names
    write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
  }
}

mapping()