Count the number of sequences or the total number of amino acids in a fasta file

countseqs

#!/bin/bash

count_nseqs() {
    file="$1"
    if [ -f "$file" ]; then
        if [[ "$file" == *.gz ]]; then
            count=$(zcat "$file" | grep -c "^>")
        else
            count=$(grep -c "^>" "$file")
        fi
        echo "$count"
    else
        echo "File does not exist: $file" >&2
        exit 1
    fi
}

count_ntoks() {
    file="$1"
    if [ -f "$file" ]; then
        if [[ "$file" == *.gz ]]; then
            sum=0
            zcat "$file" | awk '/^>/ { if (seq != "") { sum += length(seq) } seq = "" } /^>/ {next} { seq = seq $0 } END { sum += length(seq); print sum }'
        else
            sum=0
            awk '/^>/ { if (seq != "") { sum += length(seq) } seq = "" } /^>/ {next} { seq = seq $0 } END { sum += length(seq); print sum }' "$file"
        fi
    else
        echo "File does not exist: $file" >&2
        exit 1
    fi
}

# Main script
if [ $# -eq 0 ]; then
    echo "Usage: ./fasta_length.sh [-ntok] <fasta_file>"
    exit 1
fi

file_flag=""
fasta_file=""

# Parse command-line arguments
while [ "$1" != "" ]; do
    case $1 in
        -ntok )         file_flag="ntok"
                        ;;
        * )             fasta_file="$1"
    esac
    shift
done


if [ "$file_flag" == "ntok" ]; then
    count_ntoks "$fasta_file"
else
    count_nseqs "$fasta_file"
fi