mappability_filter

#! /usr/bin/env ruby
#
# Vivek Rai
# vivekrai@umich.edu
# (c) Parker Lab
#
# July 26, 2018
#

require 'optparse'
require 'ostruct'


options = OpenStruct.new

blacklist = {
  'hg19' => [
    '/lab/data/reference/human/hg19/annot/wgEncodeDacMapabilityConsensusExcludable.bed.gz',
    '/lab/data/reference/human/hg19/annot/wgEncodeDukeMapabilityRegionsExcludable.bed.gz'
  ],
  'mm9' => [
    '/lab/work/vivekrai/data/reference/mouse/mm9/annot/mm9.blacklist.bed' 
  ]
}


pargs = OptionParser.new do |opts|
  opts.banner = <<~BANNER

  USAGE: mappability_filter [BED] [-w] [-b]

  Accepts input from a BED file (.gz allowed) or STDIN. Prints to STDOUT.

  BANNER

  # opts.on('-w', '--whitelist', Array, "Whitelist BED files") do |v|
  #   options.whitelist = options.whitelist.push(v)
  # end

  opts.on('-g', '--genome', "Genome (mm9, hg19)") do |v|
    options.genome = v
    puts(v)
    if v.nil? or v.empty?
      options.genome = 'hg19'
    end
  end

  opts.on('-b', '--blacklist', Array, "=MANDATORY", "Blacklist BED files") do |v|
    options.blacklist = v
  end
end.parse!

blacklist = blacklist[options.genome].push(options.blacklist)

input = (STDIN.tty?) ? pargs.first : 'stdin'

#check_bedtools = `which bedtools`

#if check_bedtools.empty?
#  STDERR.syswrite "ERROR: bedtools not found. Exiting!"
#  exit(1)

STDERR.syswrite <<-MSG
Using blacklists:
- #{blacklist.join "\n- "}
MSG

STDOUT.syswrite `intersectBed -a #{input} -b #{options.blacklist.join ' '} -v`