Count nucleotides in a sequence (from file or standard input).

count-nuc.sh

#!/usr/bin/env bash

set -e
set -u

input="${1-/dev/stdin}"

declare -A counts=(
    [A]=0
    [C]=0
    [G]=0
    [T]=0)

while read line < "$input"; do
    for nuc in A C G T; do
        counts[$nuc]=$((${counts[$nuc]} +
                        $(sed "s/[^$nuc]//g" <<< "$line" | xargs echo -n | wc -c)))
    done
done

for nuc in ${!counts[@]}; do
    echo "$nuc  ${counts[$nuc]}"
done