R/utils.R

In bernatgel/regioneR: Association analysis of genomic regions based on permutation tests

getSeparator <- function(l, seps=c("\t", ",", ";")) {
  #Check all seps and find the one where all rows are split into the same 
  #number of elements and said number is bigger than 1 and it's the largest
  num.fields <- unlist(lapply(seps, function(sep) {
    split.length <- unlist(lapply(strsplit(x = l, split = sep), length))
    if(split.length[1]>1 && all(split.length==split.length[1])) return(split.length[1])
    else return(-1)
  }))
  max.sep <- IRanges::which.max(num.fields)[1]  #if more than one sep is equally good, chose the first one
  if(num.fields[max.sep]>1) return(seps[max.sep])
  return(NULL)
}
 

hasHeader <- function(l, sep) {
  #Check if the first line does not contain numerics (since this is expected 
  #to be used by toGRanges, we expect there will be numeric columns)
  nums <- suppressWarnings(as.numeric(strsplit(x = l[1], split = sep)[[1]]))
  return(all(is.na(nums)))
}

#Supports only single line comments
firstNonCommentLine <- function(file.name, comment.char="#") {
  pattern <- paste0("^", comment.char)
  step <- 100
  total <- step
  previous.num.lines <- 0
  ll <- readLines(file.name, n = total)
  while(all(grepl(pattern, ll)) && length(ll)>previous.num.lines) {
    previous.num.lines <- length(ll)
    total <- total + step
    ll <- readLines(file.name, n = total)
  }
  if(all(grepl(pattern, ll))) return(NULL)
  return(which(!grepl(pattern, ll))[1])
}