unpac

#! /usr/bin/env bash

info() {
cat <<EOF

  Converts PacBio bam files into fasta or fastq format using bam2fastx
  provided by PacBio https://github.com/PacificBiosciences/bam2fastx
  MUST have bam2fastx installed (simple via conda)

  [usage]:	unpac -f <fastq/a> -o <outfile.name> -d <working.directory>
  [example]: 	unpac -f fasta -o pangolin_1  -d ./pangolin_pbio

  -f <fastX>      | fasta or fastq file output
  -o <outfile>    | output filename prefix
  -d <directory>  | path to working directory

EOF
}

usage() {
cat <<EOF

[usage]:	unpac -f fastq/a -o <outfile.name> -d <working.directory>
[example]: 	unpac -f fasta -o armadillo  -d ./

EOF
}

if [[ -z "$1" ]]; then
  info
  exit 1
fi

fastq(){
  echo "output file will be named $OUTFILE.fq.gz"
  bam2fastq -o $OUTFILE $SUBREADS
    if [ $SCRAPS == "y" ] ; then
        bam2fastq -o $OUTFILE $SCRAPFILES
    fi
}
export -f fastq
fasta(){
  echo "output file will be named $OUTFILE.fa.gz" 
  bam2fasta -o $OUTFILE $SUBREADS
  if [ $SCRAPS == 'y' ] ; then
      bam2fasta -o $OUTFILE $SCRAPFILES
  fi
}
export -f fasta

while getopts ":f:o:d:" opt; do
  case $opt in
    f)
      FASTX=$OPTARG
      if [ "$FASTX" != 'fastq' ] && [ "$FASTX" != 'fasta' ] ; then
        echo -e "\n\t :::Please specify either fasta or fastq:::"
        usage
        exit 1
      fi
      ;;
    o)
      OUTFILE=$OPTARG
      ;;
    d)
      WORKDIR=$OPTARG
      ;;
	\?)
      echo "Invalid option: -$OPTARG" >&2
      usage
      exit 1
      ;;
    :)
      echo "-$OPTARG requires an argument." >&2
      usage
      exit 1
      ;;
  esac
done

SUBREADS=$(find $WORKDIR -name "*.subreads.bam")
echo "Do you want to process scraps.bam files too (y/n)? "
  read -r SCRAPS
  if [ $SCRAPS == "y" ] ; then
    SCRAPFILES=$(find $WORKDIR -name "*.scraps.bam")
  fi

if [ $FASTX == "fastq" ] ; then
  fastq 
else
  fasta
fi

exit 1