--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_features.R	Mon Nov 12 11:10:16 2018 -0500
@@ -0,0 +1,167 @@
+# Read file and return file content as data.frame
+read_file <- function(path,header){
+  file <- try(read.table(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="", check.names = F),silent=TRUE)
+  if (inherits(file,"try-error")){
+    stop("File not found !")
+  }else{
+    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
+    return(file)
+  }
+}
+
+order_columns <- function (df,ncol,id_type,file){
+  if (id_type=="Uniprot_AC"){ncol=dim.data.frame(file)[2]}
+  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 = strsplit(list, "[ \t\n]+")[[1]]
+  list = list[list != ""]    #remove empty entry
+  list = gsub("-.+", "", list)  #Remove isoform accession number (e.g. "-2")
+  return(list)
+}
+
+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
+        --nextprot: path to nextprot information file
+        --column: the column number which you would like to apply...
+        --header: true/false if your file contains a header
+        --type: the type of input IDs (Uniprot_AC/EntrezID)
+        --pc_features: IsoPoint,SeqLength,MW
+        --localization: Chr,SubcellLocations
+        --diseases_info: Diseases
+        --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)
+  }
+}
+
+# Get information from neXtProt
+get_nextprot_info <- function(nextprot,input,pc_features,localization,diseases_info){
+  if(diseases_info){
+    cols = c("NextprotID",pc_features,localization,"Diseases")
+  } else {
+    cols = c("NextprotID",pc_features,localization)
+  }
+  
+  cols=cols[cols!="None"]
+  info = nextprot[match(input,nextprot$NextprotID),cols]
+  return(info)
+}
+
+protein_features = function() {
+
+  args <- get_args()  
+  
+  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_human_protein_features/args.rda")
+  #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_human_protein_features/args.rda")
+  
+  #setting variables
+  inputtype = args$inputtype
+  if (inputtype == "copy_paste") {
+    input = get_list_from_cp(args$input)
+    input = input[input!=""]
+  } else if (inputtype == "file") {
+    filename = args$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_file(filename, header)                                                      # Get file content
+    input = sapply(file[,ncol],function(x) strsplit(as.character(x),";")[[1]][1],USE.NAMES = F)     # Extract Protein IDs list
+    if (args$type == "NextprotID" && ! "NextprotID" %in% colnames(file)) { colnames(file)[ncol] <- "NextprotID" 
+    } else if (args$type == "NextprotID" && "NextprotID" %in% colnames(file) && match("NextprotID",colnames(file))!=ncol ) { 
+      colnames(file)[match("NextprotID",colnames(file))] <- "old_NextprotID" 
+      colnames(file)[ncol] = "NextprotID"
+    }
+  }
+
+  # Read reference file
+  nextprot = read_file(args$nextprot,T)
+  
+  # Parse arguments
+  id_type = args$type
+  pc_features = strsplit(args$pc_features, ",")[[1]]
+  localization = strsplit(args$localization, ",")[[1]]
+  diseases_info = str2bool(args$diseases_info)
+  output = args$output
+
+  # Change the sample ids if they are Uniprot_AC ids to be able to match them with
+  # Nextprot data
+  if (id_type=="Uniprot_AC"){
+    NextprotID = gsub("^","NX_",input)
+    if (inputtype == "file" && "NextprotID" %in% colnames(file)){colnames(file)[match("NextprotID",colnames(file))] <- "old_NextprotID"}
+    file = cbind(file,NextprotID)
+    } else if (id_type=="NextprotID") {
+    if (inputtype == "file") {
+      NextprotID = file$NextprotID
+    } else {
+      NextprotID = input
+    }
+  }
+
+  # Select user input protein ids in nextprot
+  if ((length(NextprotID[NextprotID %in% nextprot[,1]]))==0){
+    write.table("None of the input ids can be found in Nextprot",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
+  } else {
+    res <- get_nextprot_info(nextprot,NextprotID,pc_features,localization,diseases_info)
+    
+    # Write output
+    if (inputtype == "copy_paste") {
+      if (id_type=="Uniprot_AC"){
+        output_content = cbind(input, res)
+        colnames(output_content)[1] = id_type
+      }
+      if ("res" %in% colnames(output_content)){colnames(output_content)[which(colnames(output_content)=="res")] = "NexprotID" } #if no features are selected
+    } else if (inputtype == "file") {
+      res = res[!duplicated(res$NextprotID),]
+      output_content = merge(file, res,by="NextprotID",incomparables = NA,all.x=T)
+      output_content = order_columns(output_content,ncol,id_type,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)
+  } 
+  
+}
+protein_features()