--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GO_prof_comp.R	Thu Feb 28 05:53:47 2019 -0500
@@ -0,0 +1,180 @@
+options(warn=-1)  #TURN OFF WARNINGS !!!!!!
+suppressMessages(library(clusterProfiler,quietly = TRUE))
+
+#return the number of character from the longest description found (from the 10 first)
+max_str_length_10_first <- function(vector){
+  vector <- as.vector(vector)
+  nb_description = length(vector)
+  if (nb_description >= 10){nb_description=10}
+  return(max(nchar(vector[1:nb_description])))
+}
+
+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)
+  }
+}
+
+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("Selection and Annotation HPA
+      Arguments:
+      --inputtype1: type of input (list of id or filename)
+      --inputtype2: type of input (list of id or filename)
+      --input1: input1
+      --input2: input2
+      --column1: the column number which you would like to apply...
+      --column2: the column number which you would like to apply...
+      --header1: true/false if your file contains a header
+      --header2: true/false if your file contains a header
+      --ont: ontology to use
+      --lev: ontology level
+      --org: organism db package
+      --list_name1: name of the first list
+      --list_name2: name of the second list \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)
+}
+
+get_ids=function(inputtype, input, ncol, header) {
+
+    if (inputtype == "text") {
+      ids = strsplit(input, "[ \t\n]+")[[1]]
+    } else if (inputtype == "file") {
+      header=str2bool(header)
+      ncol=get_cols(ncol)
+      csv = read.csv(input,header=header, sep="\t", as.is=T)
+      ids=csv[,ncol]
+    }
+
+    ids = unlist(strsplit(ids,";"))
+    ids = ids[which(!is.na(ids))]
+
+    return(ids)
+}
+
+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)
+  }
+}
+
+check_ids <- function(vector,type) {
+  uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"
+  entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
+  if (type == "entrez")
+    return(grepl(entrez_id,vector))
+  else if (type == "uniprot") {
+    return(grepl(uniprot_pattern,vector))
+  }
+}
+
+make_dotplot<-function(res.cmp,ontology) {
+  
+  res.cmp@compareClusterResult$Description <- sapply(as.vector(res.cmp@compareClusterResult$Description), function(x) {ifelse(nchar(x)>50, substr(x,1,50),x)},USE.NAMES = FALSE)
+  output_path= paste("GO_profiles_comp_",ontology,".png",sep="")
+  png(output_path,height = 720, width = 600)
+	p <- dotplot(res.cmp, showCategory=30)
+	print(p)
+	dev.off()
+}
+
+get_cols <-function(input_cols) {
+  input_cols <- gsub("c","",gsub("C","",gsub(" ","",input_cols)))
+  if (grepl(":",input_cols)) {
+    first_col=unlist(strsplit(input_cols,":"))[1]
+    last_col=unlist(strsplit(input_cols,":"))[2]
+    cols=first_col:last_col
+  } else {
+    cols = as.integer(unlist(strsplit(input_cols,",")))
+  }
+  return(cols)
+}
+
+#to check
+cmp.GO <- function(l,fun="groupGO",orgdb, ontology, level=3, readable=TRUE) {
+  cmpGO<-compareCluster(geneClusters = l,
+                        fun=fun, 
+                        OrgDb = orgdb, 
+                        ont=ontology, 
+                        level=level, 
+                        readable=TRUE)
+  
+  return(cmpGO)
+}
+
+check_ids <- function(vector,type) {
+  uniprot_pattern = "^([OPQ][0-9][A-Z0-9]{3}[0-9]|[A-NR-Z][0-9]([A-Z][A-Z0-9]{2}[0-9]){1,2})$"
+  entrez_id = "^([0-9]+|[A-Z]{1,2}_[0-9]+|[A-Z]{1,2}_[A-Z]{1,4}[0-9]+)$"
+  if (type == "entrez")
+    return(grepl(entrez_id,vector))
+  else if (type == "uniprot") {
+    return(grepl(uniprot_pattern,vector))
+  }
+}
+
+main = function() {
+  
+  #to get the args of the command line
+  args=get_args()  
+  
+  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/GO_terms_profiles_comparison/args.rda")
+  #load("/home/dchristiany/proteore_project/ProteoRE/tools/GO_terms_profiles_comparison/args.rda")
+  
+  ids1<-get_ids(args$inputtype1, args$input1, args$column1, args$header1) 
+  ids2<-get_ids(args$inputtype2, args$input2, args$column2, args$header2)
+  ont = strsplit(args$ont, ",")[[1]] 
+  lev=as.integer(args$lev)
+  org=args$org
+  
+  #load annot package 
+  suppressMessages(library(args$org, character.only = TRUE, quietly = TRUE))
+  
+  # Extract OrgDb
+  if (args$org=="org.Hs.eg.db") {
+    orgdb<-org.Hs.eg.db
+  } else if (args$org=="org.Mm.eg.db") {
+    orgdb<-org.Mm.eg.db
+  } else if (args$org=="org.Rn.eg.db") {
+    orgdb<-org.Rn.eg.db
+  }
+
+  for(ontology in ont) {
+    liste = list("l1"=ids1,"l2"=ids2)
+    names(liste) = c(args$list_name1,args$list_name2)
+    res.cmp<-cmp.GO(l=liste,fun="groupGO",orgdb, ontology, level=lev, readable=TRUE)
+    make_dotplot(res.cmp,ontology)  
+    output_path = paste("GO_profiles_comp_",ontology,".tsv",sep="")
+    write.table(res.cmp@compareClusterResult, output_path, sep="\t", row.names=F, quote=F)
+  }
+  
+} #end main 
+
+main()
+