annotate add_protein_features_mouse.R @ 2:1dea4e5f638f draft default tip

planemo upload commit 4ba1ebe7b3f5e3fabf78b5fed7ed0b92e2cbf9e5-dirty

options(warn=-1)  #TURN OFF WARNINGS !!!!!!

# Read file and return file content as data.frame
order_columns <- function (df,ncol,file){
  if (ncol==1){ #already at the right position
    return (df)
  } else {
    df = df[,c(2:ncol,1,(ncol+1):dim.data.frame(df)[2])]
  }
  return (df)
}

get_list_from_cp <-function(list){
  list = gsub(";","\t",list)
  list = strsplit(list, "[ \t\n]+")[[1]]
  list = gsub("NA","",list)
  list = list[list != ""]    #remove empty entry
  list = gsub("-.+", "", list)  #Remove isoform accession number (e.g. "-2")
  return(list)
}

check_ids <- function(vector,type) {
  uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"
  entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
  if (type == "entrez")
    return(grepl(entrez_id,vector))
  else if (type == "uniprot") {
    return(grepl(uniprot_pattern,vector))
  }
}

get_args <- function(){
  
  ## Collect arguments
  args <- commandArgs(TRUE)
  
  ## Default setting when no arguments passed
  if(length(args) < 1) {
    args <- c("--help")
  }
  
  ## Help section
  if("--help" %in% args) {
    cat("Selection and Annotation HPA
        Arguments:
        --inputtype: type of input (list of id or filename)
        --input: input
        --uniprot_file: path to uniprot reference file
        --column: the column number which you would like to apply...
        --header: true/false if your file contains a header
        --pc_features: IsoPoint,SeqLength,MW
        --output: text output filename \n")
    
    q(save="no")
  }
  
  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)
}

str2bool <- function(x){
  if (any(is.element(c("t","true"),tolower(x)))){
    return (TRUE)
  }else if (any(is.element(c("f","false"),tolower(x)))){
    return (FALSE)
  }else{
    return(NULL)
  }
}

#take data frame, return  data frame
split_ids_per_line <- function(line,ncol){
  
  #print (line)
  header = colnames(line)
  line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol])
  
  if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) {
    if (length(line)==1 ) {
      lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F)
    } else {
      if (ncol==1) {                                #first column
        lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)]))
      } else if (ncol==length(line)) {                 #last column
        lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";"))))
      } else {
        lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)]))
      }
    }
    colnames(lines)=header
    return(lines)
  } else {
    return(line)
  }
}

#create new lines if there's more than one id per cell in the columns in order to have only one id per line
one_id_one_line <-function(tab,ncol){
  
  if (ncol(tab)>1){
    
    tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x))
    header=colnames(tab)
    res=as.data.frame(matrix(ncol=ncol(tab),nrow=0))
    for (i in 1:nrow(tab) ) {
      lines = split_ids_per_line(tab[i,],ncol)
      res = rbind(res,lines)
    }
  }else {
    res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
    res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
    colnames(res)=colnames(tab)
  }
  return(res)
}

# Get information from neXtProt
get_uniprot_info <- function(ids,pc_features,uniprot_file){
    
  cols = c("Entry",pc_features)
  cols=cols[cols!="None"]
  info = uniprot_file[match(ids,uniprot_file$Entry),cols]
  colnames(info)[1]="UniProt-AC"
  
  return(info)
}

main <- function() {

  args <- get_args()  
  
  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_protein_features_mouse/args.rda")
  #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_protein_features_mouse/args.rda")
  
  #setting variables
  inputtype = args$inputtype
  if (inputtype == "copy_paste") {
    ids = get_list_from_cp(args$input)
    
    #Check for UniProt-AC ids
    if (all(!check_ids(ids,'uniprot'))){
      stop ("No UniProt-AC found in ids.")
    } else if (any(!check_ids(ids,'uniprot'))) {
      print ('Some ids in ids are not uniprot-AC:')
      print (ids[which(!check_ids(ids,'uniprot'))])
    }
    file = data.frame(ids,stringsAsFactors = F)
    ncol=1
    
  } else if (inputtype == "file") {
    filename = args$input
    ncol = args$column
    # Check ncol
    if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
      stop("Please enter an integer for level")
    } else {
      ncol = as.numeric(gsub("c", "", ncol))
    }
    
    header = str2bool(args$header)
    file = read.table(filename, header = header , sep = "\t", fill = TRUE, stringsAsFactors = FALSE, quote="", check.names = F, comment.char = "")                                                  # Get file content
    if (any(grep(";",file[,ncol]))) {file = one_id_one_line(file,ncol)}
    ids=file[,ncol]
  }

  # Read reference file
  uniprot_file <- read.table(args$uniprot_file, header = TRUE , sep = "\t", fill = TRUE,stringsAsFactors = FALSE, quote="", check.names = F, comment.char = "")

  # Parse arguments
  pc_features = gsub("__ob__","[",gsub("__cb__","]",strsplit(args$pc_features, ",")[[1]]))
  output = args$output
  
  #output file
  res <- get_uniprot_info(ids,pc_features,uniprot_file)
  res = res[!duplicated(res$`UniProt-AC`),]
  output_content = merge(file, res,by.x=ncol,by.y="UniProt-AC",incomparables = NA,all.x=T)
  output_content = order_columns(output_content,ncol,file)
  output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" et " " to NA
  write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
    
} 

if(!interactive()) {
  main()
}