tacseq

#!/bin/bash

# set default values to arguments
MISMATCHES=5  # default mismatches
UMI=2  # default UMI threshold

# tacseq command usage function
tacseq_usage() {
  echo "usage: $0 [options] <command>"
  echo "TAC-seq data analysis"
  echo ""
  echo "options:"
  echo "  -h  display this help and exit"
  echo ""
  echo "commands:"
  echo "  prep  prepare samples (FASTQ files) for counting"
  echo "  count  count reads and molecules per sample and target"
  echo ""
}

# prep sub-command usage function
prep_usage() {
  echo "usage: $0 $subcommand [options]"
  echo "Prepare samples (FASTQ files) for counting."
  echo ""
  echo "mandatory:"
  echo "  -i  input file: gzip compressed/uncompressed FASTQ file or '-' as standard input (stdin)"
  echo "  -t  target file: target file format is based on FASTX Barcode Splitter barcode file format (http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_barcode_splitter_usage)"
  echo "  -o  output directory"
  echo ""
  echo "optional:"
  echo "  -h  display this help and exit"
  echo "  -m  mismatches: number of allowed mismatches per target sequence (default: 5)"
  echo ""
}

# count sub-command usage function
count_usage() {
  echo "usage: $0 $subcommand [options]"
  echo "Count reads and molecules per sample and target."
  echo ""
  echo "mandatory:"
  echo "  -i  input directory: 'tacseq prep' output directory"
  echo ""
  echo "optional:"
  echo "  -h  display this help and exit"
  echo "  -u  UMI threshold (default: 2)"
  echo ""
}

# parse options to sub-commands
subcommand="$1"
OPTIND=2
case "$subcommand" in
  # parse options to 'prep' sub-command
  prep )
    while getopts ":i:t:o:m:" opt; do
      case ${opt} in
        i )
          INPUT=$OPTARG
          ;;
        t )
          TARGET=$OPTARG
          ;;
        o )
          OUTPUT=$OPTARG
          ;;
        m )  # optional
          MISMATCHES=$OPTARG
          ;;
    * )
      prep_usage 1>&2
      exit 1
      ;;
      esac
    done
  shift $((OPTIND-1))

  # check for mandatory options
  if [ ! "$INPUT" ] || [ ! "$TARGET" ] || [ ! "$OUTPUT" ]; then
    prep_usage 1>&2
    exit 1
  fi

  # run 'prep' sub-command
  source prep.sh "$INPUT" "$TARGET" "$OUTPUT" $MISMATCHES
    ;;
  # parse options to 'count' sub-command
  count )
    while getopts ":i:u:" opt; do
      case ${opt} in
        i )
          INPUT=$OPTARG
          ;;
        u )  # optional
          UMI=$OPTARG
          ;;
    * )
      count_usage 1>&2
      exit 1
      ;;
      esac
    done
  shift $((OPTIND-1))

  # check for mandatory options
  if [ ! "$INPUT" ]; then
    count_usage 1>&2
    exit 1
  fi

  # run 'count' sub-command
  source count.sh "$INPUT" $UMI
    ;;
  * )
    tacseq_usage 1>&2
    exit 1
    ;;
esac