--- a/kegg_identification.R	Fri Jan 24 10:46:35 2020 -0500
+++ b/kegg_identification.R	Mon May 17 12:29:42 2021 +0000
@@ -1,19 +1,19 @@
-options(warn=-1)  #TURN OFF WARNINGS !!!!!!
+options(warn = -1)  #TURN OFF WARNINGS !!!!!!
 
 suppressMessages(library(KEGGREST))
 
-get_args <- function(){
-  
+get_args <- function() {
+
   ## Collect arguments
   args <- commandArgs(TRUE)
-  
+
   ## Default setting when no arguments passed
-  if(length(args) < 1) {
+  if (length(args) < 1) {
     args <- c("--help")
   }
-  
+
   ## Help section
-  if("--help" %in% args) {
+  if ("--help" %in% args) {
     cat("Pathview R script
     Arguments:
       --help                  Print this test
@@ -24,180 +24,201 @@
       --nb_pathways           number of pathways to return
       --header                boolean
       --output                output path
-      --species               species used to get specific pathways (hsa,mmu,rno)
+      --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")
+      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
-  
+
+  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{
+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")){
+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{
+  }else {
     return(file)
   }
 }
 
-get_pathways_list <- function(species){
+get_pathways_list <- function(species) {
   ##all available pathways for the species
-  pathways <-keggLink("pathway", species)
-  tot_path<-unique(pathways)
-  
+  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)
+  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 = gsub("[[:blank:]]|\u00A0|NA","",list)
-  list = list[which(!is.na(list[list != ""]))]    #remove empty entry
-  list = unique(gsub("-.+", "", list))  #Remove isoform accession number (e.g. "-2")
+get_list_from_cp <- function(list) {
+  list <- strsplit(list, "[ \t\n]+")[[1]]
+  list <- gsub("[[:blank:]]|\u00A0|NA", "", list)
+  list <- list[which(!is.na(list[list != ""]))]    #remove empty entry
+  list <- unique(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)
+geneid_to_kegg <- function(vector, species) {
+  vector <- sapply(vector, function(x) paste(species, x, sep = ":"),
+                   USE.NAMES = F)
+  return(vector)
 }
 
-to_keggID <- function(id_list,id_type){
-  if (id_type == "ncbi-geneid") {                              
-    id_list <-  unique(geneID_to_kegg(id_list,args$species))
-  } else if (id_type=="uniprot"){
-    id_list <- unique(sapply(id_list, function(x) paste(id_type,":",x,sep=""),USE.NAMES = F))
-    if (length(id_list)>250){
-      id_list <- split(id_list, ceiling(seq_along(id_list)/250))
-      id_list <- sapply(id_list, function(x) keggConv("genes",x))
+to_keggid <- function(id_list, id_type) {
+  if (id_type == "ncbi-geneid") {
+    id_list <-  unique(geneid_to_kegg(id_list, args$species))
+  }else if (id_type == "uniprot") {
+    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))
       id_list <- unique(unlist(id_list))
     } else {
       id_list <- unique(keggConv("genes", id_list))
     }
-  } else if (id_type=="kegg-id") {
+  } else if (id_type == "kegg-id") {
     id_list <- unique(id_list)
   }
-  return (id_list)
+  return(id_list)
 }
 
 #take data frame, return  data frame
-split_ids_per_line <- function(line,ncol){
-  
+split_ids_per_line <- function(line, ncol) {
+
   #print (line)
-  header = colnames(line)
-  line[ncol] = gsub("[[:blank:]]|\u00A0","",line[ncol])
-  
-  if (length(unlist(strsplit(as.character(line[ncol]),";")))>1) {
-    if (length(line)==1 ) {
-      lines = as.data.frame(unlist(strsplit(as.character(line[ncol]),";")),stringsAsFactors = F)
+  header <- colnames(line)
+  line[ncol] <- gsub("[[:blank:]]|\u00A0", "", line[ncol])
+
+  if (length(unlist(strsplit(as.character(line[ncol]), ";"))) > 1) {
+    if (length(line) == 1) {
+      lines <- as.data.frame(unlist(strsplit(
+        as.character(line[ncol]), ";")), stringsAsFactors = F)
     } else {
-      if (ncol==1) {                                #first column
-        lines = suppressWarnings(cbind(unlist(strsplit(as.character(line[ncol]),";")), line[2:length(line)]))
-      } else if (ncol==length(line)) {                 #last column
-        lines = suppressWarnings(cbind(line[1:ncol-1],unlist(strsplit(as.character(line[ncol]),";"))))
+      if (ncol == 1) {        #first column
+        lines <- suppressWarnings(cbind(unlist(strsplit(
+          as.character(line[ncol]), ";")), line[2:length(line)]))
+      } else if (ncol == length(line)) {         #last column
+        lines <- suppressWarnings(cbind(line[1:ncol - 1],
+                          unlist(strsplit(as.character(line[ncol]), ";"))))
       } else {
-        lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)]))
+        lines <- suppressWarnings(cbind(line[1:ncol - 1],
+          unlist(strsplit(as.character(line[ncol]), ";"), use.names = F),
+          line[(ncol + 1):length(line)]))
       }
     }
-    colnames(lines)=header
+    colnames(lines) <- header
     return(lines)
   } else {
     return(line)
   }
 }
 
-#create new lines if there's more than one id per cell in the columns in order to have only one id per line
-one_id_one_line <-function(tab,ncol){
-  
-  if (ncol(tab)>1){
-    
-    tab[,ncol] = sapply(tab[,ncol],function(x) gsub("[[:blank:]]","",x))
-    header=colnames(tab)
-    res=as.data.frame(matrix(ncol=ncol(tab),nrow=0))
-    for (i in 1:nrow(tab) ) {
-      lines = split_ids_per_line(tab[i,],ncol)
-      res = rbind(res,lines)
+#create new lines if there's more than one id per cell in the columns in order
+#to have only one id per line
+one_id_one_line <- function(tab, ncol) {
+
+  if (ncol(tab) > 1) {
+
+    tab[, ncol] <- sapply(tab[, ncol], function(x) gsub("[[:blank:]]", "", x))
+    header <- colnames(tab)
+    res <- as.data.frame(matrix(ncol = ncol(tab), nrow = 0))
+    for (i in seq_len(nrow(tab))) {
+      lines <- split_ids_per_line(tab[i, ], ncol)
+      res <- rbind(res, lines)
     }
-  }else {
-    res = unlist(sapply(tab[,1],function(x) strsplit(x,";")),use.names = F)
-    res = data.frame(res[which(!is.na(res[res!=""]))],stringsAsFactors = F)
-    colnames(res)=colnames(tab)
+  } else {
+    res <- unlist(sapply(tab[, 1], function(x) strsplit(x, ";")), use.names = F)
+    res <- data.frame(res[which(!is.na(res[res != ""]))], stringsAsFactors = F)
+    colnames(res) <- colnames(tab)
   }
   return(res)
 }
 
-kegg_mapping<- function(kegg_id_list,id_type,ref_ids) {
-  
+kegg_mapping <- function(kegg_id_list, id_type, ref_ids) {
+
     #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))
-    
+    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]]$NAME,USE.NAMES = FALSE)
-    
-    res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)]))
-    res <- res[order(as.numeric(res[,3]),decreasing = TRUE),]
-    colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb KEGG genes IDs mapped in the pathway", "nb total of KEGG genes IDs present in the pathway")
-    
+    path_names <- names(in_path[which(in_path != 0)])
+    name <- sapply(path_names, function(x) keggGet(x)[[1]]$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_identification/args.Rda")
-#load("/home/dchristiany/proteore_project/ProteoRE/tools/kegg_identification/args.Rda")
-
 ###setting variables
-header = str2bool(args$header)
-if (!is.null(args$id_list)) {id_list <- get_list_from_cp(args$id_list)}           #get ids from copy/paste input
-if (!is.null(args$input)) {                                                       #get ids from input file
-  csv <- read_file(args$input,header)
-  ncol <- as.numeric(gsub("c", "" ,args$id_column))
-  csv <- one_id_one_line(csv,ncol)
-  id_list <- as.vector(csv[,ncol])
-  id_list <- unique(id_list[which(!is.na(id_list[id_list!=""]))])
+header <- str2bool(args$header)
+if (!is.null(args$id_list)) {
+  id_list <- get_list_from_cp(args$id_list)
+  }     #get ids from copy/paste input
+if (!is.null(args$input)) { #get ids from input file
+  csv <- read_file(args$input, header)
+  ncol <- as.numeric(gsub("c", "", args$id_column))
+  csv <- one_id_one_line(csv, ncol)
+  id_list <- as.vector(csv[, ncol])
+  id_list <- unique(id_list[which(!is.na(id_list[id_list != ""]))])
 }
 
 #convert to keggID if needed
-id_list <- to_keggID(id_list,args$id_type)
+id_list <- to_keggid(id_list, args$id_type)
 
 #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$nb_pathways,] }
+res <- kegg_mapping(id_list, args$id_type, pathways_list)
+if (nrow(res) > as.numeric(args$nb_pathways)) {
+  res <- res[1:args$nb_pathways, ]
+  }
 
-write.table(res, file=args$output, quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE)
-
+write.table(res, file = args$output, quote = FALSE, sep = "\t",
+            row.names = FALSE, col.names = TRUE)

--- a/kegg_identification.xml	Fri Jan 24 10:46:35 2020 -0500
+++ b/kegg_identification.xml	Mon May 17 12:29:42 2021 +0000
@@ -1,4 +1,4 @@
-<tool id="kegg_identification" name="KEGG pathways mapping and coverage" version="2020.01.23">
+<tool id="kegg_identification" name="KEGG pathways mapping and coverage" version="2021.04.12">
     <description>[PathView]</description>
     <requirements>
         <requirement type="package" version="1.18.0">bioconductor-keggrest</requirement>