Why do I have “join: extra operand ‘/dev/fd/62′” error?

I have a script equijoin2:

#! /bin/bash

# default args                                                                                                                                                                    
delim="," # CSV by default                                                                                                                                                        
outer=""
outerfile=""
# Parse flagged arguments:                                                                                                                                                        
while getopts "o:td:" flag
do
  case $flag in
    d) delim=$OPTARG;;
    t) delim="t";;
    o) outer="-a $OPTARG";;
    ?) exit;;
  esac
done
# Delete the flagged arguments:                                                                                                                                                   
shift $(($OPTIND -1))
# two input files                                                                                                                                                                 
f1="$1"
f2="$2"
# cols from the input files                                                                                                                                                       
col1="$3"
col2="$4"


join "$outer" -t "$delim" -1 "$col1" -2 "$col2" <(sort "$f1") <(sort "$f2")

and two files

$ cat file1
c c1
b b1
$ cat file2
a a2
c c2
b b2

Why does the last command fail? Thanks.

$ equijoin2 -o 2  -d " " file1 file2 1 1
a a2
b b1 b2
c c1 c2
$ equijoin2 -o 1  -d " " file1 file2 1 1
b b1 b2
c c1 c2
$ equijoin2   -d " " file1 file2 1 1
join: extra operand '/dev/fd/62'

Answers:

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Method 1

"$outer" is a quoted scalar variable so it always expands to one argument. If empty or unset, that still expands to one empty argument to join (and when you call your script with -o2, that’s one -a 2 argument instead of the two arguments -a and 2).

Your join is probably GNU join in that it accepts options after non-option arguments. That "$outer" is a non-option argument when empty as it doesn’t start with - so is treated as a file name and join complains about the third file name provided which it doesn’t expect.

If you want a variable with a variable number of arguments, use an array:

outer=()
...
(o)
   outer=(-a "$OPTARG");;

...
join "${outer[@]}"

Though here you could also do:

outer=
...
(o)
   outer="-a$OPTARG";;
...
join ${outer:+"$outer"} ... <(sort < "$f1") <(sort < "$f2")

Or:

unset -v outer
...
(o)
   outer="$OPTARG";;
...
join ${outer+-a "$outer"} ...

(that one doesn’t work in zsh except in sh/ksh emulation).

Some other notes:

• join -t 't' doesn’t work. You’d need delim=$'t' to store a literal TAB in $delim
• Remember to use -- when passing arbitrary arguments to commands (or use redirections where possible). So sort -- "$f1" or better sort < "$f1" instead of sort "$f1".
• arithmetic expansions are also subject to split+glob so should also be quoted (shift "$((OPTIND - 1))") (here not a problem though as you’re using bash which doesn’t inherit $IFS from the environment and you’re not modifying IFS earlier in the script, but still good practice).

All methods was sourced from stackoverflow.com or stackexchange.com, is licensed under cc by-sa 2.5, cc by-sa 3.0 and cc by-sa 4.0