uf-freqs

#!/bin/sh
#
#  uf-freqs - Count frequencies in unfasta files
#  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] [FILE ...]

  Count frequencies of elements in each sequence in each unfasta FILE and write
  to standard output.  If no FILE is present or when FILE is '-', read standard
  input.

  Options
   -b, --bare         Do not output the headers, only the data
   -l, --length-only  Length of sequence only, no frequencies per element
   -t, --totals       Write totals across all sequences at bottom
   -i, --ignore-case  Count all lower case letters as upper case
" >&2
    exit ${1:-1}
}

# Parse options

BARE=0
LENGTH_ONLY=0
TOTALS=0
IGNORE_CASE=0

while [ $# -ne 0 -a "$(expr "$1" : '\(.\)..*')" = "-" ]; do
    case $1 in
    -b|--b*) BARE=1 ;;
    -l|--l*) LENGTH_ONLY=1 ;;
    -t|--t*) TOTALS=1 ;;
    -i|--i*) IGNORE_CASE=1 ;;
    -h|--h*) usage_exit 0 ;;
    *) usage_exit ;;
    esac
    shift || usage_exit
done

gawk -bO -v P="$(basename "$0")" -v BARE=$BARE -v LENGTH_ONLY=$LENGTH_ONLY -v TOTALS=$TOTALS -v IGNORE_CASE=$IGNORE_CASE '
BEGIN { PROCINFO["sorted_in"] = "@ind_str_asc" }
NR%2==1 && !BARE 
NR%2==0 {
    if (IGNORE_CASE) $0 = toupper($0)
    for (i=1; i<=length($0); ++i) freqs[substr($0,i,1)] += 1
    printf length($0)
    if (!LENGTH_ONLY) for (j in freqs) printf " " j "=" freqs[j]
    printf "\n"
    if (TOTALS) {
        for (j in freqs) totals[j] += freqs[j]
        grand_total += length($0)
    }
    for (j in freqs) freqs[j] = 0
}
END { 
    if (TOTALS) {
        if (!BARE) print ">TOTALS"
        printf grand_total;
        if (!LENGTH_ONLY) for (j in totals) printf " " j "=" totals[j]
        printf "\n"
    }
} 
' "$@"

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