comparison goprofiles.R @ 4:715002a394ec draft

planemo upload commit b36435833bf54f90f62cc240f2cda1c889161b23-dirty

3:ed226f0e5625

# Load necessary libraries
library(org.Hs.eg.db)
library(goProfiles)

# Read file and return file content as data.frame?
readfile = function(filename, header) {
  if (header == "true") {
    # Read only the first line of the files as data (without headers):
    headers <- read.table(filename, nrows = 1, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = 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)
    # Remove empty rows
    file <- file[!apply(is.na(file) | file == "", 1, all),]
    #And assign the headers of step two to the data:
    names(file) <- headers
  }
  else {
    file <- read.table(filename, header = FALSE, sep = "\t", stringsAsFactors = FALSE, fill = TRUE)
  }
  return(file)
}

getprofile = function(ids, id_type, level, duplicate) {

  args <- as.list(as.character(argsDF$V2))
  names(args) <- argsDF$V1

  input_type = args$input_type
  if (input_type == "text") {
    input = strsplit(args$input, " ")[[1]]
  }
  else if (input_type == "file") {
    filename = args$input
    ncol = args$ncol
    # Check ncol

4:715002a394ec

# Load necessary libraries
library(org.Hs.eg.db)
library(goProfiles)

# 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 = "")
    #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 = "")
    # 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 = "")
    # Remove empty rows
    file <- file[!apply(is.na(file) | file == "", 1, all), , drop=FALSE]
  }
  return(file)
}

getprofile = function(ids, id_type, level, duplicate) {

  args <- as.list(as.character(argsDF$V2))
  names(args) <- argsDF$V1

  input_type = args$input_type
  if (input_type == "text") {
    input = strsplit(args$input, "[ \t\n]+")[[1]]
  }
  else if (input_type == "file") {
    filename = args$input
    ncol = args$ncol
    # Check ncol