diff add_protein_features_mouse.R @ 0:1e856941a888 draft

planemo upload commit 8de59a5dbf9206fa3d9f7a1c07e79ccb792b3e3f-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_protein_features_mouse.R	Fri Feb 08 08:46:04 2019 -0500
@@ -0,0 +1,186 @@
+# Read file and return file content as data.frame
+order_columns <- function (df,ncol,file){
+  if (ncol==1){ #already at the right position
+    return (df)
+  } else {
+    df = df[,c(2:ncol,1,(ncol+1):dim.data.frame(df)[2])]
+  }
+  return (df)
+}
+
+get_list_from_cp <-function(list){
+  list = strsplit(list, "[ \t\n]+")[[1]]
+  list = gsub("NA","",list)
+  list = list[list != ""]    #remove empty entry
+  list = gsub("-.+", "", list)  #Remove isoform accession number (e.g. "-2")
+  return(list)
+}
+
+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))
+  }
+}
+
+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:
+        --inputtype: type of input (list of id or filename)
+        --input: input
+        --uniprot_file: path to uniprot reference file
+        --column: the column number which you would like to apply...
+        --header: true/false if your file contains a header
+        --pc_features: IsoPoint,SeqLength,MW
+        --output: text output filename \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)
+  }
+}
+
+#take data frame, return  data frame
+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)
+    } 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]),";"))))
+      } else {
+        lines = suppressWarnings(cbind(line[1:ncol-1], unlist(strsplit(as.character(line[ncol]),";"),use.names = F), line[(ncol+1):length(line)]))
+      }
+    }
+    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)
+    }
+  }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)
+}
+
+# Get information from neXtProt
+get_uniprot_info <- function(ids,pc_features,uniprot_file){
+    
+  cols = c("Entry",pc_features)
+  cols=cols[cols!="None"]
+  info = uniprot_file[match(ids,uniprot_file$Entry),cols]
+  colnames(info)[1]="UniProt-AC"
+  
+  return(info)
+}
+
+main <- function() {
+
+  args <- get_args()  
+  
+  #save(args,file="/home/dchristiany/proteore_project/ProteoRE/tools/add_protein_features_mouse/args.rda")
+  #load("/home/dchristiany/proteore_project/ProteoRE/tools/add_protein_features_mouse/args.rda")
+  
+  #setting variables
+  inputtype = args$inputtype
+  if (inputtype == "copy_paste") {
+    ids = get_list_from_cp(args$input)
+    
+    #Check for UniProt-AC ids
+    if (all(!check_ids(ids,'uniprot'))){
+      stop ("No UniProt-AC found in ids.")
+    } else if (any(!check_ids(ids,'uniprot'))) {
+      print ('Some ids in ids are not uniprot-AC:')
+      print (ids[which(!check_ids(ids,'uniprot'))])
+    }
+    file = data.frame(ids,stringsAsFactors = F)
+    ncol=1
+    
+  } else if (inputtype == "file") {
+    filename = args$input
+    ncol = args$column
+    # Check ncol
+    if (! as.numeric(gsub("c", "", ncol)) %% 1 == 0) {
+      stop("Please enter an integer for level")
+    } else {
+      ncol = as.numeric(gsub("c", "", ncol))
+    }
+    
+    header = str2bool(args$header)
+    file = read.table(filename, header = header , sep = "\t", fill = TRUE, stringsAsFactors = FALSE, quote="", check.names = F, comment.char = "")                                                  # Get file content
+    if (any(grep(";",file[,ncol]))) {file = one_id_one_line(file,ncol)}
+    ids=file[,ncol]
+  }
+
+  # Read reference file
+  uniprot_file <- read.table(args$uniprot_file, header = TRUE , sep = "\t", fill = TRUE,stringsAsFactors = FALSE, quote="", check.names = F, comment.char = "")
+
+  # Parse arguments
+  pc_features = gsub("__ob__","[",gsub("__cb__","]",strsplit(args$pc_features, ",")[[1]]))
+  output = args$output
+  
+  #output file
+  res <- get_uniprot_info(ids,pc_features,uniprot_file)
+  res = res[!duplicated(res$`UniProt-AC`),]
+  output_content = merge(file, res,by.x=ncol,by.y="UniProt-AC",incomparables = NA,all.x=T)
+  output_content = order_columns(output_content,ncol,file)
+  output_content <- as.data.frame(apply(output_content, c(1,2), function(x) gsub("^$|^ $", NA, x)))  #convert "" et " " to NA
+  write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
+    
+} 
+
+if(!interactive()) {
+  main()
+}