uf-take

#!/bin/sh
#
#  uf-take - Take characters from head of unfasta format sequences.
#  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

# 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] NUM [FILE ...]

  For each sequence in each unfasta format FILE write the first NUM characters
  to standard output.  If no FILE is present or when FILE is '-', read standard
  input.  With modifier -b|--but, take all except the final NUM characters.

  Options
   -b, --but   Copy everything BUT the final NUM characters from each sequence.
   -m, --mark  Document the edit by appending '(uf:take:[but:]NUM)' to headers.
" >&2
    exit ${1:-1}
}

# Parse options

BUT=0
MARK=0

while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
    case $1 in
    -m|--mark) MARK=1 ;;
    -b|--but)  BUT=1 ;;
    -h|--help) usage_exit 0 ;;
    *) usage_exit ;;
    esac
    shift || usage_exit
done

# Check first argument is positive number

[ $# -ge 1 -a "$(expr "$1" : '\([0-9]\+\)')" = "$1" ] || usage_exit

NUM=$1
shift

# Delegate to gawk

gawk -bO -v P="$(basename "$0")" -v N=$NUM -v M=$MARK -v B=$BUT '
    NR%2==1 { print $0 (M ? " (uf:take:" (B?"but:":"") N ")" : "") }
    NR%2==0 { print B ? substr ($0,1,length($0)-N) : substr ($0,1,N) }
    ' "$@"

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