#!/bin/bash
#plot_profile.sh

script_name="plot_profile.sh"

#Help function
usage() {
  echo "-h  --Help documentation for $script_name"
  echo "-g  --File path to gtf/bed files"
  echo "Example: $script_name -g 'genome.gtf'"
  exit 1
}


raise()
{
  echo "${1}" >&2
}

check_tools() {
  raise "
   Checking for required libraries and components on this system
   "
   deeptools --version &> version_deeptools.txt
   if [ $? -gt 0 ]
     then
      raise "Missing deeptools"
      return 1
    fi
}

compute_matrix() {
  raise "
  Computing matrix on ${1} using ${2}
  "

  computeMatrix reference-point \
    --referencePoint TSS \
    -S ${1} \
    -R ${2} \
    --skipZeros \
    -o computeMatrix.gz \
    -p max/2

  if [ $? -gt 0 ]
  then
    raise "Problem building matrix"
    return 1
  fi
}

plot_profile() {
  raise "
  Plotting profile
  "

  plotProfile -m computeMatrix.gz \
    -out plotProfile.png

  if [ $? -gt 0 ]
  then
    raise "Problem plotting"
    return 1
  fi
}


run_main() {

  # Parsing options
  OPTIND=1 # Reset OPTIND
<<<<<<< HEAD
  while getopts :g:h opt
=======
  while getopts g:h opt
>>>>>>> 61db854ac1fcdb60431ad48a0a5cab0255d9c2d3
      do
          case $opt in
              g) gtf=$OPTARG;;
              h) usage;;
          esac
      done

  shift $(($OPTIND -1))

  # Check for mandatory options
  if [[ -z $gtf ]]; then
      usage
  fi

  bws=$(ls *.pooled.fc_signal.bw)

  check_tools || exit 1

  compute_matrix "${bws}" "${gtf}" || return 1

  plot_profile || return 1

  raise "ALL COMPLETE"
}

if [[ "${BASH_SOURCE[0]}" == "${0}" ]]
then
  run_main "$@"
  if [ $? -gt 0 ]
  then
    exit 1
  fi
fi