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I have read some entries regarding this question like in here or here, but I haven't been able to make my code work. It should be very simple.

I need to append items from a while loop, after a small transformation, to an empty list. My code is as follows:

folder='/path/to/directories/'

ls  $folder | while read dir ; do
    if [[ $dir =~ ANF-* ]]; then
        names=()

        ls $folder/$dir/FASTQS  | while read file ; do
            name=$(echo $file | cut -d "_" -f 1-3 )
            echo $name
            names+=("$name")
        done
        echo ${names[*]}   #Also tried echo ${names[@]}
    fi
done

The first 'echo' works so it gets through the conditional and into the second loop.

I have also tried using 'declare -a' to create the empty array.

If I try to append $file to the list it does not work either.

I think the problem is the appending action because if I create an array that is not empty I got the array's items in the second 'echo'.

Thanks a lot in advance. RX

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  • 3
    See also BashFAQ/024. Commented Mar 14, 2019 at 12:56
  • As a side note, instead of using ls (the output of which is notoriously brittle), you should use globs: for dir in "$folder"/*; do, which solves both the setting-variable-in-a-subprocess problem and is robust with respect to filenames. Commented Mar 14, 2019 at 12:57
  • Furthermore, ANF-* as a regular expression means ANF, ANF-, ANF--, ANF--- etc., which probably isn't what you meant. If you meant "starts with ANF-, you should have used ^ANF-.* (.* for "any number of any character"), or just ^ANF- because =~ checks submatches; or [[ $dir == ANF-* ]] (shell patterns instead of regex). Commented Mar 14, 2019 at 13:00
  • And finally, I don't think you need a nested loop; you could do something like for file in "$folder"/ANF-*/FASTQS/*; do, and depending on what the filenames look like, you could probably use parameter expansion to get the parts you want. Commented Mar 14, 2019 at 13:03
  • I will try, but I don't think that's the problem, I got into the loop and I get the files I am interested in modified, the problem is with appending the names to the list. Commented Mar 14, 2019 at 13:08

1 Answer 1

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Try to wrap your echo with double quotes:

folder='/path/to/directories/'

ls  $folder | while read dir ; do
    if [[ $dir =~ ANF-* ]]; then
        names=()
        local iteration=1
        ls $folder/$dir/FASTQS  | while read file ; do
            name=$(echo $file | cut -d "_" -f 1-3 )
            echo $name
            names+=("$name")
            echo "iteration $iteration"
            iteration=$((iteration+1))
            declare -p names
        done
        echo "${names[@]}"
        # you can show the array like this:
        declare -p names
    fi
done

Your names array is being altered, but when the loop terminates, the alterations go away. Look at the answers @Benjamin W. kindly pointed.

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5 Comments

Thanks a lot, but I have added your modifications but it is still not working.. The items of the of the loop are not being added to the list. The loop is working I get the list of files of the directories I am interested in, and I am able to modify the names inside the loop.
Quoting has nothing to do with it; the problem is modifying a variable in a subshell.
@Rachael, your question was edited by a moderator (@Benjamin W.), and it points to a former answer... have you checked it out ?
Not a moderator, just a fellow user :) And the question wasn't edited, but marked as a duplicate.
The problem is modified without any problem, the problem is appending the item not modifying it.

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