remove nonprintables and improve read

hipathia/convert_to_hipathia.R

@@ -98,6 +98,7 @@ get_hipathia_files <- function(raw_sif, node_prefix, model_elements, target_dir)
   
   att_nodes <- sort(unique(c(raw_sif[,1],raw_sif[,3])))
   att_labels <- sapply(att_nodes, function(x) with(model_elements, name[elementId == x]))
+  att_labels <- gsub("[^ -~]+", "", att_labels)
   node_ID <- paste0("N-",node_prefix,"-", att_nodes)
   ### Retrieve Entrez and type for the entire list of unique nodes
   entrez <- sapply(att_nodes, group_elements, model_elements, all_entrez)

hipathia/reduce_hipathia_graph.R

@@ -56,8 +56,8 @@ create_hipathia_graph <- function(hipathia_attributes, hipathia_sif) {
 
 ### A function to return graph object from the att and sif files
 read_hipathia_graph <- function(file_name, prefix){
-  hats <- read.table(paste0(prefix, file_name, ".att"), sep = "\t", header = T, stringsAsFactors = F)
-  hsif <- read.table(paste0(prefix,file_name, ".sif"), sep = "\t", header = T, stringsAsFactors = F)
+  hats <- read.table(paste0(prefix, file_name, ".att"), sep = "\t", header = T, stringsAsFactors = F, quote = "")
+  hsif <- read.table(paste0(prefix,file_name, ".sif"), sep = "\t", header = T, stringsAsFactors = F, quote = "")
   create_hipathia_graph(hats, hsif)
 }