how to make an argument optional in getopt bash

Question

I want to make an argument as optional in getopt bash so that if the user didn't specify it, then it still runs without killing the program. How can i do that. Here is my previous code

while getopts ":l:q:s:e:hg:" opt; do
  case $opt in
    l)
      lincRNAfasta=$OPTARG
    ;;
    q)
      query_species=$OPTARG
      ;;
    s)
      subject_species=$OPTARG
      ;;
    e)
      subject_gff=$OPTARG
      ;;
    h)
      echo "USAGE : open script in text editor"
      exit 1
      ;;
    g)
      subject_genome=$OPTARG
      ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      exit 1
      ;;
    :)
      echo "Option -$OPTARG requires an argument." >&2
      exit 1
      ;;
  esac
done

What do you mean by 'optional argument'? If the user doesn't specify, for example, `-s species-name`, then the variable `subject_species` won't be set by this code. You can default it to a suitable value before the loop, or you can diagnose its absence after the loop (and take steps not to pass the non-existent value to the remainder of the script -- or the program executed by the remainder of the script). If you want to allow the user to type `-s` without a value after it, you need to define what it means to do that ("I want you to choose a species, but I'm not going to tell you which one?") — Jonathan Leffler, Mar 24 '15 at 00:38

jmunsch · Accepted Answer · 2015-03-24T00:52:36.853

Sorry, had to update my answer, I misunderstood the question.

I was looking at the documentation for getopts.c which does support ::

But the code that you have works whether I specify 1, 2, or 3 arguments, and in any order.

If it is exiting with an error one reason could be that the variables need to be defined:

#! /bin/bash
lincRNAfasta=
query_species=
subject_species=
subject_gff=
subject_genome=

help='''
  USAGE : open script in text editor
    -l lincRNAfasta
    -q query_species
    -s subject_species
    -e subject_gff
    -g subject_genome
'''

while getopts ":l:q:s:e:hg:" opt; do
  case $opt in
    l)
      lincRNAfasta=$OPTARG
    ;;
    q)
      query_species=$OPTARG
      ;;
    s)
      subject_species=$OPTARG
      ;;
    e)
      subject_gff=$OPTARG
      ;;
    h)
      printf "$help"
      exit 1
      ;;
    g)
      subject_genome=$OPTARG
      ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      exit 1
      ;;
    :)
      echo "Option -$OPTARG requires an argument." >&2
      exit 1
      ;;
  esac
done

echo "doing something else"

if [ -z "$lincRNAfasta" ];then
    echo "its empty"
    echo "lincRNAfasta: $lincRNAfasta"
    echo
else
    echo "not empty"
    echo "lincRNAfasta: $lincRNAfasta"
    echo
fi

if [ -z "$query_species" ];then
    echo "its empty"
    echo "query_species: $query_species"
    echo
else
    echo "not empty"
    echo "query_species: $query_species"
    echo
fi

if [ -z "$subject_species" ];then
    echo "its empty"
    echo "subject_species: $subject_species"
    echo
else
    echo "not empty"
    echo "subject_species: $subject_species"
    echo
fi

if [ -z "$subject_gff" ];then
    echo "its empty"
    echo "subject_gff: $subject_gff"
    echo
else
    echo "not empty"
    echo "subject_gff: $subject_gff"
    echo
fi

if [ -z "$subject_genome" ];then
    echo "its empty"
    echo "subject_genome: $subject_genome"
    echo
else
    echo "not empty"
    echo "subject_genome: $subject_genome"
    echo
fi


# do something once variables have been set
# any variable not set will be empty

echo "doing something else"

Output:

bob@squids:~/Desktop$ ./1.sh -h

  USAGE : open script in text editor
    -l lincRNAfasta
    -q query_species
    -s subject_species
    -e subject_gff
    -g subject_genome
bob@squids:~/Desktop$ ./1.sh -s a -g h -e e -q q
doing something else
its empty
lincRNAfasta: 

not empty
query_species: q

not empty
subject_species: a

not empty
subject_gff: e

not empty
subject_genome: h

doing something else
bob@squids:~/Desktop$ ./1.sh -s a -g h -e e
doing something else
its empty
lincRNAfasta: 

its empty
query_species: 

not empty
subject_species: a

not empty
subject_gff: e

not empty
subject_genome: h

doing something else
bob@squids:~/Desktop$ ./1.sh -s a -e e -g 123
doing something else
its empty
lincRNAfasta: 

its empty
query_species: 

not empty
subject_species: a

not empty
subject_gff: e

not empty
subject_genome: 123

doing something else

Or instead of initializing the variables as empty, you could initialize them as a string like "NOTSPECIFIEDONSTART". And when starting the script you could pass an empty string like -g ''

for example if i wanted to make `subject_gff` as optional argument, shall i do this `::e` ? — upendra, Mar 24 '15 at 00:01
I updated the answer. I initially misunderstood the question. So by declaring the arguments at the beginning, each flag would then be optional, but each of the arguments still exists, and because of this would be "optional". — jmunsch, Mar 24 '15 at 00:33

how to make an argument optional in getopt bash

1 Answers1

Linked