seqcount

#!/bin/bash
helpstr="SEQCOUNT - Count number of sequences in a FASTA/FASTQ file
Usage: seqcount [option] ... SEQ_FILE

Positional arguments:
 1. FASTA or FASTQ file to count
The script will automaticall detect whether the input is a FASTA or FASTQ
file from the header character (> or @).

Options (defaults):
 -r: Reference file to calculate percentage
 -h: Display this help message and exit

If a reference file is specified, the script will return the number of
sequences in the file in both absolute form and as a percentage of
the number of sequences in the reference file."

unset fastq refq ref_file seq_file
while [ $OPTIND -le $# ]; do
    # Optional arguments
    while getopts "r:qQh" opt; do
        case "$opt" in
            q)
                fastq="true"
                ;;
            Q)
                refq="true"
                ;;
            r)
                ref_file=$OPTARG
                ;;
            # Else:
            h)
                echo "$helpstr"
                exit
                ;;
            *)
                echo "Invalid argument:" $opt >&2
                echo "$helpstr"
                exit 1
        esac
    done
    # Positional arguments:
    if [[ -z "$seq_file" ]]; then
        seq_file=${@:$OPTIND:1}
        OPTIND=$(expr $OPTIND + 1)
    fi
done
shift $((OPTIND-1))

#Argument errors and warnings:
if [[ -z $seq_file ]]; then
    >&2 echo "Error: FASTA or FASTQ input file required."
    echo "$helpstr"
    exit 1
fi

# Find number of sequences:
headchar=$(awk '/./{print;exit}' "$seq_file" | cut -c1)
if [[ "$headchar" == ">" ]]; then
    factor=2
elif [[ "$headchar" == "@" ]]; then
    factor=4
else
    >&2 echo "Error: Input file must be in FASTA or FASTQ format."
    exit 1
fi
nlines=$(egrep -v '^$' "$seq_file" | wc -l) # Excludes blank lines
seqnum=$(expr $nlines / $factor)

if [[ -n "$ref_file" ]]; then
    rchar=$(awk '/./{print;exit}' "$ref_file" | cut -c1)
    if [[ "$rchar" == ">" ]]; then
        rfactor=2
    elif [[ "$rchar" == "@" ]]; then
        rfactor=4
    else
        >&2 echo "Error: Reference file must be in FASTA or FASTQ format."
        exit 1
    fi
    rlines=$(egrep -v '^$' "$ref_file" | wc -l) # Excludes blank lines
    refnum=$(expr $rlines / $rfactor)
    # Print percentage
    x=$(expr 100 \* $seqnum)
    y=$refnum
    perc=$(echo -| awk -v x=$x -v y=$y '{printf "%.2f\n", x/y}')%
    echo "$seqnum ($perc)"
else
    echo $seqnum
fi
exit