diff add_expression_HPA.R @ 6:71214d6034e7 draft

planemo upload commit 4af7ac25de19ca10b1654820e909c647a2d337b2-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/add_expression_HPA.R	Mon Mar 19 10:09:01 2018 -0400
@@ -0,0 +1,121 @@
+# Read file and return file content as data.frame
+readfile = function(filename, header) {
+  if (header == "true") {
+    # Read only first line of the file as header:
+    headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "", comment.char = "")
+    #Read the data of the files (skipping the first row)
+    file <- read.table(filename, skip = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "", comment.char = "")
+    # Remove empty rows
+    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
+    #And assign the header to the data
+    names(file) <- headers
+  }
+  else {
+    file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings=c("", "NA"), blank.lines.skip = TRUE, quote = "", comment.char = "")
+    # Remove empty rows
+    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
+  }
+  return(file)
+}
+
+add_expression = function(input, atlas, options) {
+  if (all(!input %in% atlas$Ensembl)) {
+    return(NULL)
+  }
+  else {
+    res = matrix(nrow=length(input), ncol=0)
+    names = c()
+    for (opt in options) {
+      names = c(names, opt)
+      info = atlas[match(input, atlas$Ensembl,incomparable="NA"),][opt][,]
+      res = cbind(res, info)
+    }
+    colnames(res) = names
+    return(res)
+  }
+}
+
+main = function() {
+  args <- commandArgs(TRUE)
+  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: either a file name (e.g : input.txt) or a list of blank-separated
+                 ENSG identifiers (e.g : ENSG00000283071 ENSG00000283072)
+        --atlas: path to protein atlas file
+        --column: the column number which you would like to apply...
+        --header: true/false if your file contains a header
+        --select: information from HPA to select, maybe: 
+                  RNA.tissue.category,Reliability..IH.,Reliability..IF. (comma-separated)
+        --output: text output filename \n")
+    q(save="no")
+  }
+  
+  # Parse arguments
+  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
+
+  inputtype = args$inputtype
+  if (inputtype == "copypaste") {
+    input = strsplit(args$input, " ")[[1]]
+  }
+  else if (inputtype == "tabfile") {
+    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 = args$header
+    # Get file content
+    file = readfile(filename, header)
+    # Extract Protein IDs list
+    input = c()
+    for (row in as.character(file[,ncol])) {
+      input = c(input, strsplit(row, ";")[[1]][1])
+    }
+  }
+
+  # Read protein atlas
+  protein_atlas = args$atlas
+  protein_atlas = readfile(protein_atlas, "true")
+
+  # Add expression
+  output = args$output
+  names = c()
+  options = strsplit(args$select, ",")[[1]]
+  res = add_expression(input, protein_atlas, options)
+
+  # Write output
+  if (is.null(res)) {
+    write.table("None of the input ENSG ids are can be found in HPA data file",file=output,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
+  }
+  else {
+    if (inputtype == "copypaste") {
+      names = c("Ensembl", colnames(res))
+      res = cbind(as.matrix(input), res)
+      colnames(res) = names
+      write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE)
+    }
+    else if (inputtype == "tabfile") {
+      names = c(names(file), colnames(res))
+      output_content = cbind(file, res)
+      colnames(output_content) = names
+      write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
+    }
+  }
+
+}
+
+main()