--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compute_kegg_pathways.R	Mon Nov 12 10:59:49 2018 -0500
@@ -0,0 +1,152 @@
+options(warn=-1)  #TURN OFF WARNINGS !!!!!!
+
+suppressMessages(library(KEGGREST))
+
+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("Pathview R script
+    Arguments:
+      --help                  Print this test
+      --input                 tab file
+      --id_list               id list ',' separated
+      --id_type               type of input ids (kegg-id, uniprot_AC,geneID)
+      --id_column             number og column containg ids of interest
+      --nb_pathways           number of pathways to return
+      --header                boolean
+      --output                output path
+      --species               species used to get specific pathways (hsa,mmu,rno)
+
+      Example:
+      Rscript keggrest.R --input='P31946,P62258' --id_type='uniprot' --id_column 'c1' --header TRUE \n\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)
+  }
+}
+
+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)
+  }
+}
+
+get_pathways_list <- function(species){
+  ##all available pathways for the species
+  pathways <-keggLink("pathway", species)
+  tot_path<-unique(pathways)
+  
+  ##formating the dat into a list object
+  ##key= pathway ID, value = genes of the pathway in the kegg format
+  pathways_list <- sapply(tot_path, function(pathway) names(which(pathways==pathway)))
+  return (pathways_list)
+}
+
+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)
+}
+
+geneID_to_kegg <- function(vector,species){
+  vector <- sapply(vector, function(x) paste(species,x,sep=":"),USE.NAMES = F)
+  return (vector)
+}
+
+kegg_mapping<- function(kegg_id_list,id_type,ref_ids) {
+  
+    #convert to KEGG ID
+    #if (id_type!="kegg-id"){
+    #  id_list <- unique(sapply(id_list, function(x) paste(id_type,":",x,sep=""),USE.NAMES = F))
+    #  if (length(id_list)>250){
+    #    id_list <- split(id_list, ceiling(seq_along(id_list)/250))
+    #    id_list <- sapply(id_list, function(x) keggConv("genes",x))
+    #    kegg_id_list <- unique(unlist(id_list))
+    #  } else {
+    #  kegg_id_list <- unique(keggConv("genes", id_list))
+    #  }
+    #} else {
+    #  kegg_id_list <- unique(id_list)
+    #}
+  
+    #mapping
+    map<-lapply(ref_ids, is.element, unique(kegg_id_list))
+    names(map) <- sapply(names(map), function(x) gsub("path:","",x),USE.NAMES = FALSE)    #remove the prefix "path:"
+    
+    in.path<-sapply(map, function(x) length(which(x==TRUE)))
+    tot.path<-sapply(map, length)
+    
+    ratio <- (as.numeric(in.path[which(in.path!=0)])) / (as.numeric(tot.path[which(in.path!=0)]))
+    ratio <- as.numeric(format(round(ratio*100, 2), nsmall = 2))
+    
+    ##useful but LONG
+    ## to do before : in step 1
+    path.names<-names(in.path[which(in.path!=0)])
+    name <- sapply(path.names, function(x) keggGet(x)[[1]]$NAME,USE.NAMES = FALSE)
+    
+    res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)]))
+    res <- res[order(as.numeric(res[,3]),decreasing = TRUE),]
+    colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb KEGG genes IDs mapped in the pathway", "nb total of KEGG genes IDs present in the pathway")
+    
+    return(res)
+    
+}
+
+#get args from command line
+args <- get_args()
+
+#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_identification/args.Rda")
+#load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_pathways_identification/args.Rda")
+
+###setting variables
+header = str2bool(args$header)
+if (!is.null(args$id_list)) {id_list <- get_list_from_cp(args$id_list)}
+if (!is.null(args$input)) { 
+  csv <- read_file(args$input,header)
+  ncol <- as.numeric(gsub("c", "" ,args$id_column))
+  id_list <- as.vector(csv[,ncol])
+  id_list <- id_list[which(!is.na(id_list))]
+}
+if (args$id_type == "ncbi-geneid") {
+  id_list <-  geneID_to_kegg(id_list,args$species)
+}
+
+
+#get pathways of species with associated KEGG ID genes
+pathways_list <- get_pathways_list(args$species)
+
+#mapping on pathways
+res <- kegg_mapping(id_list,args$id_type,pathways_list)
+if (nrow(res) > as.numeric(args$nb_pathways)) { res <- res[1:args$nb_pathways,] }
+
+write.table(res, file=args$output, quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE)
+