rc

#!/bin/env bash
set -e
helpstr="RC - reverse-complement a nucleotide sequence or FASTA file.
Can handle base ambiguity codes.
Usage:
  rc SEQUENCE
  rc -f FILE

Options:
 -f: Treat input as a filepath rather than a nucleotide sequence.
 -h: Print this help message and exit.
"

unset filein input
while [ $OPTIND -le $# ]; do
    while getopts "fh" opt; do
        case "$opt" in
            f)
                filein="true"
                ;;
            h)
                echo "$helpstr"
                exit
                ;;
            *)
                echo "Invalid argument:" $opt >&2
                echo "$helpstr"
                exit 1
        esac
    done
    if [[ -z "$input" ]]; then
        input=${@:$OPTIND:1}
        OPTIND=$(expr $OPTIND + 1)
    fi
done
shift $((OPTIND-1))

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

# Script:

in="[ATUGCatugcNnKMRYSWkmryswBVHDbvhdXx]"
to="[TAACGtaacgNnMKYRWSmkyrwsVBDHvbdhXx]"

if [[ -z $filein ]]; then
    echo $input | tr "$in" "$to" | rev
else
    while read line; do
        nhead=$(echo "$line" | egrep '^>' | wc -l)
        if [[ $nhead -ge 1 ]]; then
            echo ${line}\|RC
        else
            echo $line | tr "$in" "$to" | rev
        fi
    done < $input
fi
exit