Bash Shell Script - Check for a Flag and Grab Its Value

Bash Shell Script - Check for a flag and grab its value

You should read this getopts tutorial.

Example with -a switch that requires an argument :

#!/bin/bash

while getopts ":a:" opt; do
  case $opt in
    a)
      echo "-a was triggered, Parameter: $OPTARG" >&2
      ;;
    \?)
      echo "Invalid option: -$OPTARG" >&2
      exit 1
      ;;
    :)
      echo "Option -$OPTARG requires an argument." >&2
      exit 1
      ;;
  esac
done

Like greybot said(getopt != getopts) :

The external command getopt(1) is never safe to use, unless you know
it is GNU getopt, you call it in a GNU-specific way, and you ensure
that GETOPT_COMPATIBLE is not in the environment. Use getopts (shell
builtin) instead, or simply loop over the positional parameters.

How to get arguments with flags in Bash

This is the idiom I usually use:

while test $# -gt 0; do
  case "$1" in
    -h|--help)
      echo "$package - attempt to capture frames"
      echo " "
      echo "$package [options] application [arguments]"
      echo " "
      echo "options:"
      echo "-h, --help                show brief help"
      echo "-a, --action=ACTION       specify an action to use"
      echo "-o, --output-dir=DIR      specify a directory to store output in"
      exit 0
      ;;
    -a)
      shift
      if test $# -gt 0; then
        export PROCESS=$1
      else
        echo "no process specified"
        exit 1
      fi
      shift
      ;;
    --action*)
      export PROCESS=`echo $1 | sed -e 's/^[^=]*=//g'`
      shift
      ;;
    -o)
      shift
      if test $# -gt 0; then
        export OUTPUT=$1
      else
        echo "no output dir specified"
        exit 1
      fi
      shift
      ;;
    --output-dir*)
      export OUTPUT=`echo $1 | sed -e 's/^[^=]*=//g'`
      shift
      ;;
    *)
      break
      ;;
  esac
done

Key points are:

• $# is the number of arguments
• while loop looks at all the arguments supplied, matching on their values inside a case statement
• shift takes the first one away. You can shift multiple times inside of a case statement to take multiple values.

bash script; searching files for threshold value in table by row and print out to file or stdout

with a lot of help I finally have a solution:

#! /bin/bash
cutoff=5.0
for i in sim_results_rep*; do

while read -r LINE; do
echo $LINE | grep 'First atom' > /dev/null
if [ $? -ne 0 ]
then
  continue 
else
 read -r LINE 
    while true; do 
      read -r LINE
      echo $LINE | grep 'Total distance penalty' > /dev/null
      if [ $? -ne 0 ] 
      then
       x=`echo "$LINE" | awk '{print $11}'` 
    if [ `echo "$x > $cutoff" | bc` == 1 ] 
    then
      echo "In file $i, the follwing distance has a penalty higher than $cutoff"
      echo $LINE
    else
      continue 

    fi

  else 
    break
    fi

  done
  break 
fi

done < $i/*.nmrout

done

Direct wrong flag input

while getopts ahs: option
do
     case "$option"
     in
        $FLAG_HELP) code/function;;
        $FLAG_TARLogs) code/function;;
        $FLAG_TARResrc) code/function ;;
        $FLAG_DELLogs) code/function;;
        $FLAG_TAREncod) code/function;;
        $FLAG_DELResrc) code/function;;
        $FLAG_DELEncod) code/function;;
        h) DisplayUsage
       exit 0;;
        ?) DisplayUsage
       exit 1;;
     esac
done 2>/dev/null

Display function contains the options and how they are used..

DisplayUsage()
{
 echo
 echo
 echo "Options are "
 echo 
 echo
 echo
 echo
}

getops $OPTARG is empty if flag value contains brackets

Short summary: Double-quote your variable references. And use shellcheck.net.

Long explanation: When you use a variable without double-quotes around it (e.g. echo ${str}), the shell tries to split its value into words, and expand anything that looks like a wildcard expression into a list of matching files. In the case of [0.0.0.0], the brackets make it a wildcard expression that'll match either the character "0" or "." (equivalent to [0.]). If you had a file named "0", it would expand to that string. With no matching file(s), it's normally left unexpanded, but with the nullglob set it expands to ... null.

Turning off nullglob solves the problem if there are no matching files, but isn't really the right way do it. I remember (but can't find right now) a question we had about a script that failed on one particular computer, and it turned out the reason was that one computer happened to have a file that matched a bracket expression in an unquoted variable's value.

The right solution is to put double-quotes around the variable reference. This tells the shell to skip word splitting and wildcard expansion. Here's an interactive example:

$ str='[0.0.0.0]'    # Quotes aren't actually needed here, but they don't hurt
$ echo $str    # This works without nullglob or a matching file
[0.0.0.0]
$ shopt -s nullglob
$ echo $str    # This fails because of nullglob

$ shopt -u nullglob
$ touch 0
$ echo $str    # This fails because of a matching file
0
$ echo "$str"    # This just works, no matter whether file(s) match and/or nullglob is set
[0.0.0.0]

So in your script, simply change the last line to:

echo "${str}"

Note that double-quotes are not required in either case $opt in or str=$OPTARG because variables in those specific contexts aren't subject to word splitting or wildcard expansion. But IMO keeping track of which contexts it's safe to leave the double-quotes off is more hassle than it's worth, and you should just double-quote 'em all.

BTW, shellcheck.net is good at spotting common mistakes like this; I recommend feeding your scripts through it, since this is probably not the only place you have this problem.

How do I grab an INI value within a shell script?

How about grepping for that line then using awk

version=$(awk -F "=" '/database_version/ {print $2}' parameters.ini)

Propagate all arguments in a Bash shell script

Use "$@" instead of plain $@ if you actually wish your parameters to be passed the same.

Observe:

$ cat no_quotes.sh
#!/bin/bash
echo_args.sh $@

$ cat quotes.sh
#!/bin/bash
echo_args.sh "$@"

$ cat echo_args.sh
#!/bin/bash
echo Received: $1
echo Received: $2
echo Received: $3
echo Received: $4

$ ./no_quotes.sh first second
Received: first
Received: second
Received:
Received:

$ ./no_quotes.sh "one quoted arg"
Received: one
Received: quoted
Received: arg
Received:

$ ./quotes.sh first second
Received: first
Received: second
Received:
Received:

$ ./quotes.sh "one quoted arg"
Received: one quoted arg
Received:
Received:
Received:

Getting error while executing a shell script to check for a particular character in each line at a specific position and if found replace it with X

Well, I'll show 2 examples hopefully they can give an idea.
Example 1

filename = "/ray/test/raymond/test2.data"
if [ -f "$filename" -a -r "$filename" ]; then
       while read -r line; do
              if [ "${line:421:1}" = 'D' ]; then
                     printf '%s%s%s\n' "${line:0:420}" 'X' "${line:422}" >> "$new_file"
              else
                     printf '%s\n' "$line" >> "$new_file"
              fi
       done < "$filename"
elif [ ! -f "$filename" ]; then
      echo 'ERROR: Not a file'
      return 1
elif [ ! -r "$filename" ]; then
     echo 'ERROR: Can not read the file'
     return 1
fi

Example 2

filename = "/ray/test/raymond/test2.data"
new_file="$filename"'_new.txt'
if [ -f "$filename" -a -r "$filename" ]; then
       output="$new_file" awk 'BEGIN { output=ENVIRON["output"] }
       {
               if(substr($0, 422, 1) == "D") {
                       $0=sprintf("%s%s%s", substr($0, 1, 421), "X", substr($0, 423))
               }
               print $0 >> output
       }' "$filename"
elif [ ! -f "$filename" ]; then
      echo 'ERROR: Not a file'
      return 1
elif [ ! -r "$filename" ]; then
     echo 'ERROR: Can not read the file'
     return 1
fi

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