diff compute_kegg_pathways.R @ 0:42d0805353b6 draft

planemo upload commit 0ce4c81e6d2f7af8c9b52f6c07e83b0319c2adb1-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/compute_kegg_pathways.R	Wed Sep 19 05:38:52 2018 -0400
@@ -0,0 +1,112 @@
+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 (uniprot_AC or geneID)
+      --id_column             number og column containg ids of interest
+      --nb_pathways           number of pathways to return
+      --header                boolean
+      --output                output path
+      --ref                  ref file (l.hsa.gene.RData, l.hsa.up.RData, l.mmu.up.Rdata)
+
+      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)
+}
+
+args <- get_args()
+
+#save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/compute_KEGG_pathways/args.Rda")
+#load("/home/dchristiany/proteore_project/ProteoRE/tools/compute_KEGG_pathways/args.Rda")
+
+##function arguments :  
+## id.ToMap = input from the user to map on the pathways = list of IDs
+## idType : must be "UNIPROT" or "ENTREZ"
+## org : for the moment can be "Hs" only. Has to evoluate to "Mm"
+
+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.table(path,header=header, sep="\t",stringsAsFactors = FALSE, quote=""),silent=TRUE)
+  if (inherits(file,"try-error")){
+    stop("File not found !")
+  }else{
+    return(file)
+  }
+}
+
+ID2KEGG.Mapping<- function(id.ToMap,ref) {
+    
+    ref_ids = get(load(ref))
+    map<-lapply(ref_ids, is.element, unique(id.ToMap))
+    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]]$NAME,USE.NAMES = FALSE)
+    
+    res<-data.frame(I(names(in.path[which(in.path!=0)])), I(name), ratio, as.numeric(in.path[which(in.path!=0)]), as.numeric(tot.path[which(in.path!=0)]))
+    res <- res[order(as.numeric(res[,3]),decreasing = TRUE),]
+    colnames(res)<-c("pathway_ID", "Description" , "Ratio IDs mapped/total IDs (%)" ,"nb genes mapped in the pathway", "nb total genes present in the pathway")
+    
+    return(res)
+    
+}
+
+###setting variables
+header = str2bool(args$header)
+if (!is.null(args$id_list)) {id_list <- strsplit(args$id_list,",")[[1]]}
+if (!is.null(args$input)) { 
+  csv <- read_file(args$input,header)
+  ncol <- as.numeric(gsub("c", "" ,args$id_column))
+  id_list <- as.vector(csv[,ncol])
+}
+id_type <- toupper(args$id_type)
+
+#mapping on pathways
+res <- ID2KEGG.Mapping(id_list,args$ref)
+if (nrow(res) > as.numeric(args$nb_pathways)) { res <- res[1:args$nb_pathways,] }
+
+write.table(res, file=args$output, quote=FALSE, sep='\t',row.names = FALSE, col.names = TRUE)
+