FLEET/makeannot.R at master · hessJ/FLEET · GitHub

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#!/usr/bin/env Rscript


# Import packages
suppressMessages(library(optparse))
suppressMessages(require(argparse))
suppressMessages(require(GenomicRanges))
suppressMessages(require(data.table))

## Auto-detect the directory name for fleet.R
initial.options <- commandArgs(trailingOnly = FALSE)

# set masthead

masthead = as.character("
==========================================================
||
|| Functional LD-interval EnrichmEnt Test (FLEET)
|| *** Custom annotation extension script ***
||
|| Jonathan L. Hess, PhD and Stephen J. Glatt, PhD (c) 2017
||
|| SUNY Upstate Medical University, PsychGENe Lab
||
|| Contact: hessjo@upstate.edu
||
|| https://github.com/hessJ/FLEET
||
|| GNU GENERAL PUBLIC LICENSE v3
===========================================================\n")

#cat(masthead, file = log_con)
cat(masthead) # display masthead


# ========================================================================
started = Sys.time()
cat("\n")
cat(paste("Start time:", started))
cat("\n")

# create parser object
parser <- ArgumentParser()

option_list = list(


  make_option(c( "--file"), type="character", default="",
              help="Path to file (.txt, .csv, .tsv, etc.) containing annotations (with chromosome and range)", metavar="character"),

  make_option(c( "--chr"), type="character", default="",
              help="Colname with chromosome", metavar="character"),

  make_option(c( "--start"), type="character", default="",
              help="Colname for start of range (base pair)", metavar="character"),

  make_option(c( "--end"), type="character", default="",
              help="Colname for end of range (base pair)", metavar="character"),

  make_option(c( "--id"), type="character", default="",
              help="Colname with annotation labels", metavar="character"),

  make_option(c( "--out"), type="character", default="",
              help="Output path for convert annotation table (GRanges object)", metavar="character")

);

opt_parser = OptionParser(option_list=option_list);
opt = parse_args(opt_parser);


convertAnnot = function() {

  cat("\nImporting annotation table...")
  guessdelim = readLines(opt$file,1)
  tab = length(strsplit( guessdelim, "[\t]")[[1]])
  space = length(strsplit( guessdelim, " ")[[1]])
  comma = length(strsplit( guessdelim, "[,]")[[1]])

  set = list(tab,space,comma)
  names(set) = c("tab","space","comma")
  delim_type = c("\t"," ", ",")
  guesser = which(set %in% max(c(tab,space,comma)))

  cat("\nGuessing that file is:",names(set[guesser]),"delimited")

  read_annot = as.data.frame(fread(opt$file, h=T, sep = delim_type[guesser], fill = T))
  if(ncol(read_annot) < 2){stop("Unexpected number of fields in:",opt$file)}

  if(unique(grepl("chr", read_annot[,colnames(read_annot) %in% opt$chr])) == FALSE){read_annot[,colnames(read_annot) %in% opt$chr] = paste("chr",read_annot[,colnames(read_annot) %in% opt$chr],sep="")}

  cat("\nConverting to GRanges object...")

  annot_gr = GRanges(seqnames = read_annot[,colnames(read_annot) %in% opt$chr],
                     IRanges(start = read_annot[,colnames(read_annot) %in% opt$start],
                             end = read_annot[,colnames(read_annot) %in% opt$end]),
                     id = read_annot[,colnames(read_annot) %in% opt$id])


  cat("\nWriting output...")
  saveRDS(annot_gr, file = paste(opt$out,".Rdata",sep=""))


}

convertAnnot()