Parsing optional and not optional arguments

I am new with bash and after reading and trying a lot about how to parse arguments I cannot what I really want to do I want to parse optional and not optional arguments. More specifically I want to parse 3 arguments, first (a fastaq file) second (a second optional fastaq file) a third argument that will be a directory.

my_script.sh -f1 file1.fasta --f2 file2.fasta -d/home/folder1/folder2 or

my_script.sh -f1 file1.fasta -d /home/folder1/folder2

I have tried to do this in many ways but I dont know how to let the program identifies when there are two fasta files and a directory and, when there is only one fasta file and a directory.

With this arguments I want to save them in variables because they will be used later by third parties.

I have tried this:



for i in "$@"; do
 case $i in
   -f1=|-fasta1=)
     FASTA1="${i#=}"
     shift # past argument=value
     ;;
   -d) DIRECTORY=$2
  shift 2
     ;;
   -d=|-directory=) DIRECTORY="${i#=}"
   shift # past argument=value
     ;;
   --f2=|-fasta2=) FASTA2="${i#*=}"
    shift # past argument=value
     ;;
   *)
     ;;
 esac
done

But I just got this

scripts_my_first_NGS]$ ./run.sh -f1 fasta.fasta -d /home/folder1
FASTA1  =
DIRECTORY     =
FASTA2     =

Solution

Basically you need to add a separate parser for versions of the options where they aren't used with the equal sign.

Also your shift commands are useless since you're processing a for loop. So convert it to to a while [[ $# -gt 0 ]]; do loop instead.

I also added a few modifications which I suggest be added.

while [[ $# -gt 0 ]]; do
    case $1 in
    -f1|-fasta1)
        FASTA1=$2
        shift
        ;;
    -f1=*|-fasta1=*)
        FASTA1=${1#*=}
        ;;
    -d|-directory)
        DIRECTORY=$2
        shift
        ;;
    -d=*|-directory=*)
        DIRECTORY=${1#*=}
        ;;
    -f2|fasta2)
        FASTA2=$2
        shift
        ;;
    -f2=*|-fasta2=*)
        FASTA2=${1#*=}
        ;;
    -*)
        echo "Invalid option: $1" >&2
        exit 1
        ;;
    --)
        # Do FILES+=("${@:2}") maybe
        break
        ;;
    *)
        # TODO
        # Do FILES+=("$1") maybe
        ;;
    esac

    shift
done

The "parser" for the with-equal and non-with-equal versions of the options can also be unified by using a helper function:

function get_opt_arg {
    if [[ $1 == *=* ]]; then
        __=${1#*=}
        return 1
    elif [[ ${2+.} ]]; then
        __=$2
        return 0 # Tells that shift is needed
    else
        echo "No argument provided to option '$1'." >&2
        exit 1
    fi
}

while [[ $# -gt 0 ]]; do
    case $1 in
    -d|-directory|-d=*|-directory=*)
        get_opt_arg "$@" && shift
        DIRECTORY=$__
        ;;
    -f1|-fasta1|-f1=*|-fasta1=*)
        get_opt_arg "$@" && shift
        FASTA1=$__
        ;;
    -f2|fasta2|-f2=*|-fasta2=*)
        get_opt_arg "$@" && shift
        FASTA2=$__
        ;;
    -*)
        echo "Invalid option: $1" >&2
        exit 1
        ;;
    --)
        # Do FILES+=("${@:2}") maybe
        break
        ;;
    *)
        # TODO
        # Do FILES+=("$1") maybe
        ;;
    esac

    shift
done

Update

I found a complete solution to command-line parsing without relying on getopt[s] and it does it even more consistently: https://konsolebox.github.io/blog/2022/05/14/general-command-line-parsing-solution-without-using-getopt-s.html