uf

#!/bin/bash
#
#  uf - Convert FASTA to unfasta format
#  Copyright (C) 2016  Marco van Zwetselaar <io@zwets.it>
#
#  This program is free software: you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation, either version 3 of the License, or
#  (at your option) any later version.
#
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
#  You should have received a copy of the GNU General Public License
#  along with this program.  If not, see <http://www.gnu.org/licenses/>.
#
#  This utility is part of http://io.zwets.it/unfasta

# "Hardened bash"
set -euo pipefail

# Function to exit this script with an error message on stderr
err_exit() { echo "$(basename "$0"): $*" >&2; exit 1; }

# Function to show usage information and exit
usage_exit() {
    echo "
Usage: $(basename $0) [OPTIONS] [FILE ...]

  Convert FILEs to unfasta format and write to standard output.  FILE must
  contain optionally gzipped FASTA data.  With no FILE or when FILE is '-',
  read standard input.  Unfasta is FASTA without the pesky line breaks.

  OPTIONS
   -r, --revert   Revert unfasta to FASTA (see below)
   -w, --width=W  Revert unfasta to FASTA with line length W (see below)
   -l, --lower    Write lowercase
   -u, --upper    Write uppercase

  Apart from checking that every sequence is preceded by a header, uf performs
  no validation of the input data.  See uf-valid.

  Options -r and -w revert sequences to classic FASTA by breaking lines at W
  (default 60) characters.  Note though that strictly there is no need to do
  this, as every unfasta file is also a valid FASTA file.  The 60 char line
  length is a recommendation, not a requirement.

  More information about the unfasta suite at http://io.zwets.it/unfasta.
" >&2
    exit ${1:-1}
}

# Parse options

REVERT=0 WIDTH=60 LOWER=0 UPPER=0 RET=0

#while (( $# )) && "$(expr "$1" : '\(.\)..*')" = "-" ]; do
while (( $# )) && [[ -z "${1%%-?*}" ]]; do
    case $1 in
    -l|--l*)  LOWER=1 ;;
    -u|--u*)  UPPER=1 ;;
    -r|--r*)  REVERT=1 ;;
    --w*=*)   WIDTH=${1##*=}; REVERT=1 ;;
    -w|--w*)  shift && WIDTH=$1; REVERT=1 ;;
    -h|--h*)  usage_exit 0 ;;
    *) usage_exit ;;
    esac
    shift || usage_exit
done

[ $# -eq 0 ] && DASH="-" || DASH=""

for F in $DASH "$@"; do
    gzip -dfc "$F" |
    if (( $REVERT )); then
        gawk -bO -v WIDTH=$WIDTH -v L=$LOWER -v U=$UPPER '
        /^>/
        /^[^>]/ { for (i=1;i<=length();i+=WIDTH) {
           S=substr($0,i,WIDTH); print (L ? tolower(S) : U ? toupper(S) : S)
        } }' '-'
    else
        gawk -bO -v L=$LOWER -v U=$UPPER 'BEGIN { ORS=""; D=0; H=0 }
        /^>/ && (H||D)     { print "\n" }
        /^>/               { print $0 "\n"; D=0; H=1 }
        /^[^>]/ && !(H||D) { print "uf: input is not valid FASTA\n" >"/dev/stderr"; exit 1 }
        /^[^>]/            { gsub(/[[:space:]]/,""); print (L ? tolower($0) : U ? toupper($0) : $0); D=1; H=0 }
        END { if (D||H) print "\n" }' '-'
    fi
done | tr -d '\r'

# vim: sts=4:sw=4:et:si:ai