--- a/add_expression_HPA.R	Wed Jan 22 15:33:21 2020 +0000
+++ b/add_expression_HPA.R	Thu Jan 23 10:44:39 2020 +0000
@@ -1,7 +1,11 @@
 # Read file and return file content as data.frame
 read_file <- function(path,header){
-  file <- read.csv(path,header=header, sep="\t",stringsAsFactors = FALSE, quote="\"", check.names = F)
-  return(file)
+  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
@@ -142,6 +146,13 @@
   }
 }
 
+convert_to_previous_header <- function(options){
+    header = c('Gene','description','Evidence','Antibody','RNA tissue specificity','Reliability (IH)','Reliability (IF)','Subcellular location','RNA tissue specific NX')
+    names(header) = c('Gene','description','Evidence','Antibody','RNA tissue category','Reliability (IH)','Reliability (IF)','Subcellular location','RNA TS TPM')
+    options = names(header[which(header %in% options)])
+    return(options)
+}
+
 main = function() {
   
   args = get_args()
@@ -176,6 +187,7 @@
   # Add expression
   output = args$output
   options = strsplit(args$select, ",")[[1]]
+  if (tail(unlist(strsplit(args$atlas,"/")),1) == "HPA_full_atlas_23-10-2018.tsv"){ options = convert_to_previous_header(options)}
   res = add_expression(ids, protein_atlas, options)
   
   # Write output