uf-hash

#!/bin/sh
#
#  uf-hash - Compute a hash over the sequence content of an unfasta file
#  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

# Defaults
ALGO="md5"

# 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 ...]

  Computes a hash over the sequence content of unfasta FILEs, or stdin if
  no FILE is present or when FILE is '-'.

  The computed hash value is invariant to changes in the sequence headers.
  It is sensitive to changes in the order of sequences in the FILE.  Pipe
  input through uf-sort to compensate for differences in sequence order.
 
  OPTIONS
   -a, --algo ALG   Use algorithm md5/sha1/224/256/384/512, default: $ALGO
" >&2
    exit ${1:-1}
}

# Parse options

unset REORDERABLE
while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
    case $1 in
    --algo=*)    ALGO=${1#--algo=} ;;
    -a|--algo*)  shift; ALGO=$1 ;;
    -h|--help)   usage_exit 0 ;;
    *) usage_exit ;;
    esac
    shift || usage_exit
done

# Check options and arguments

case $ALGO in md5|sha1|sha224|sha256|sha384|sha512) ;; *) err_exit "unknown algorithm: $ALGO" ;; esac
HASH_PGM="/usr/bin/${ALGO}sum"
[ -x "$HASH_PGM" ] || err_exit "hash program not found: $HASH_PGM (missing coreutils?)"

FILE="-"
[ $# -eq 0 ] || FILE="$1"
[ $# -lt 2 ] || usage_exit

# Do the work

gawk -bO 'NR % 2 == 0' "$FILE" | $HASH_PGM | cut -d' ' -f1

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