[WIP] ProteoRE prot_features_Uniprot_3species

tools/proteore_prot_features_3orga/.shed.yml

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+categories: [Proteomics]
+description: ProteoRE Add protein features (Human, Mouse, Rat)
+long_description: A tool for adding biochemical and cellular annotation to your protein list from UniProt
+name: proteore_prot_features_3orga
+owner: galaxyp

tools/proteore_prot_features_3orga/add_protein_features_3orga.R

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+options(warn = -1)  #TURN OFF WARNINGS !!!!!!
+
+# 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 <- gsub(";", "\t", 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 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)
+  }
+  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]
+  }
+
+
+  org <- args$org
+
+  # Read reference file
+  if (org == "Mouse") {
+    uniprot_file <- read.table(args$uniprot_file_mouse, header = TRUE,
+                               sep = "\t", fill = TRUE,
+                               stringsAsFactors = FALSE, quote = "",
+                               check.names = F, comment.char = "")
+  } else if (org == "Human") {
+    uniprot_file <- read.table(args$uniprot_file_human, header = TRUE,
+                               sep = "\t", fill = TRUE,
+                               stringsAsFactors = FALSE, quote = "",
+                               check.names = F, comment.char = "")
+  } else if (org == "Rat") {
+    uniprot_file <- read.table(args$uniprot_file_rat, 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()
+}