uf-drop

#!/bin/sh
#
#  uf-drop - Drop 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 drop the first NUM characters
  and write the remainder of the sequence to standard output.  If no FILE is
  present or when FILE is '-', read standard input.  With modifier -b|--but,
  drop all except the final NUM characters.

  Options
   -b, --but   Drop everything BUT the final NUM characters from each sequence.
   -m, --mark  Document the edit by appending '(uf:drop:[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:drop:" (B?"but:":"") N ")" : "") }
    NR%2==0 { print B ? substr ($0,length($0)-N+1) : substr ($0,N+1) }
    ' "$@"

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