diff protein_features.R @ 1:bfc679370c64 draft

planemo upload commit 5774fd6a5a746f36f6bf4671a51a39ea2b978300-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/protein_features.R	Fri Feb 16 04:06:16 2018 -0500
@@ -0,0 +1,133 @@
+# 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)
+    #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)
+    # 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)
+    # Remove empty rows
+    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
+  }
+  return(file)
+}
+
+protein_features = 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: input
+        --nextprot: path to nextprot information file
+        --column: the column number which you would like to apply...
+        --header: true/false if your file contains a header
+        --type: the type of input IDs (UniProt/EntrezID)
+        --argsP1: IsoPoint,SeqLength,MW
+        --argsP2: Chr,SubcellLocations
+        --argsP3: Diseases
+        --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$header
+    # Get file content
+    file = readfile(filename, header)
+    # Extract Protein IDs list
+    input = c()
+    for (row in as.character(file[,ncol])) {
+      input = c(input, strsplit(row, ";")[[1]][1])
+    }
+  }
+  nextprot_file = args$nextprot
+  nextprot = human_id_map = read.table(nextprot_file, header = TRUE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE, na.strings = "")
+  typeid = args$type
+  P1_args = strsplit(args$argsP1, ",")[[1]]
+  P2_args = strsplit(args$argsP2, ",")[[1]]
+  P3_args = strsplit(args$argsP3, ",")[[1]]
+  output = args$output
+
+  # Change the sample ids if they are uniprot ids to be able to match them with
+  # Nextprot data
+  if (typeid=="uniprot"){
+    input = gsub("^","NX_",input)
+  }
+
+  # Select user input protein ids in nextprot
+  if ((length(input[input %in% nextprot[,1]]))==0){
+    write.table("None of the input ids are can be found in Nextprot",file=filename,sep="\t",quote=FALSE,col.names=TRUE,row.names=FALSE)
+  } else {
+    names = c()
+    res = matrix(nrow=length(input), ncol=0)
+
+    # Get information from neXtProt
+    if (length(P1_args)>0) {
+      for (arg in P1_args) {
+        names = c(names, arg)
+        info = nextprot[match(input, nextprot["NextprotID"][,]),][arg][,]
+        res = cbind(res, info)
+      }
+    }
+    if (length(P2_args)>0) {
+      for (arg in P2_args) {
+        names = c(names, arg)
+        info = nextprot[match(input, nextprot["NextprotID"][,]),][arg][,]
+        res = cbind(res, info)
+      }
+    }
+    if (length(P3_args)>0) {
+      for (arg in P3_args) {
+        names = c(names, arg)
+        info = nextprot[match(input, nextprot["NextprotID"][,]),][arg][,]
+        res = cbind(res, info)
+      }
+    }
+
+    # Write output
+    if (inputtype == "copypaste") {
+      res = cbind(as.matrix(input), res)
+      names = c(typeid, names)
+      colnames(res) = names
+      write.table(res, output, row.names = FALSE, sep = "\t", quote = FALSE)
+    }
+    else if (inputtype == "tabfile") {
+      names = c(names(file), names)
+      output_content = cbind(file, res)
+      colnames(output_content) = names
+      write.table(output_content, output, row.names = FALSE, sep = "\t", quote = FALSE)
+    }
+  } 
+
+}
+protein_features()
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