--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_expression_HPA.R	Mon Nov 12 11:05:24 2018 -0500
@@ -0,0 +1,106 @@
+# Read file and return file content as data.frame
+read_file <- function(path,header){
+  file <- try(read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F),silent=TRUE)
+  if (inherits(file,"try-error")){
+    stop("File not found !")
+  }else{
+    return(file)
+  }
+}
+
+#convert a string to boolean
+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)
+  }
+}
+
+add_expression = function(input, atlas, options) {
+  if (all(!input %in% atlas$Ensembl)) {
+    return(NULL)
+  } else {
+    res = atlas[match(input,atlas$Ensembl),c("Ensembl",options)]
+    res <- as.data.frame(apply(res, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" et " " to NA
+    return(res)
+  }
+}
+
+main = function() {
+  args <- commandArgs(TRUE)
+  if(length(args)<1) {
+    args <- c("--help")
+  }
+  
+  # Help section
+  if("--help" %in% args) {
+    cat("Selection and Annotation HPA
+    Arguments:
+        --inputtype: type of input (list of id or filename)
+        --input: either a file name (e.g : input.txt) or a list of blank-separated
+                 ENSG identifiers (e.g : ENSG00000283071 ENSG00000283072)
+        --atlas: path to protein atlas file
+        --column: the column number which you would like to apply...
+        --header: true/false if your file contains a header
+        --select: information from HPA to select, maybe: 
+                  RNA.tissue.category,Reliability..IH.,Reliability..IF. (comma-separated)
+        --output: text output filename \n")
+    q(save="no")
+  }
+  
+  # Parse arguments
+  parseArgs <- function(x) strsplit(sub("^--", "", x), "=")
+  argsDF <- as.data.frame(do.call("rbind", parseArgs(args)))
+  args <- as.list(as.character(argsDF$V2))
+  names(args) <- argsDF$V1
+
+  save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
+  #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_expression_data_HPA/args.rda")
+  
+  inputtype = args$inputtype
+  if (inputtype == "copypaste") {
+    input = strsplit(args$input, "[ \t\n]+")[[1]]
+  } else if (inputtype == "tabfile") {
+    filename = args$input
+    ncol = args$column
+    # Check ncol
+    if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
+      stop("Please enter an integer for level")
+    } else {
+      ncol = as.numeric(gsub("c", "", ncol))
+    }
+    header = str2bool(args$header)
+    file = read_file(filename, header)
+    input =  unlist(sapply(as.character(file[,ncol]),function(x) rapply(strsplit(x,";"),c),USE.NAMES = FALSE))
+  }
+
+  # Read protein atlas
+  protein_atlas = args$atlas
+  protein_atlas = read_file(protein_atlas, T)
+
+  # Add expression
+  output = args$output
+  options = strsplit(args$select, ",")[[1]]
+  res = add_expression(input, protein_atlas, options)
+  
+
+  # Write output
+  if (is.null(res)) {
+    write.table("None of the input ENSG ids are can be found in HPA data file",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
+  } else {
+    if (inputtype == "copypaste") {
+      output_content = cbind(as.matrix(input), res)
+      colnames(output_content)[1] = "Ensembl"
+    } else if (inputtype == "tabfile") {
+      output_content = merge(file, res, by.x=ncol, by.y=1, incomparables = NA,all.x=T)
+      output_content = output_content[order(output_content[,ncol],decreasing = T),]
+    }
+  output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x)))
+  write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
+  }
+}
+
+main()