CODEWITHSUNDEEP
stringbashshellloopsunix
David Paul
David Paul

Reputation: 23

Using a loop to string together a list of variables with filenames

I have created a script that identifies a unique set of files (from a large list) and saves the file paths as unique variables (e.g. $vol1, $vol2, $vol3... see below).

for volume in `seq 1 $num_ap_files` 
    do
    bindex=$(cat ../b0_volumes_tmp.txt | head -$volume | tail -1)
    eval 'vol'${volume}=$(cat ../all_volumes.txt | head -$bindex | tail -1)
    done

I'd like to concatenate the variables into one string variable to use as input for a separate command line program. As the number of volumes may differ - it seems most appropriate to create a loop of the following nature (??? define where I am having trouble):

??? files=$vol1
for i in `seq 2 $num_ap_files
do
??? eval files=${files}" $vol"${i) 
done

I've tried a few different options here using files+=, eval function, etc. and continue to get an error message: -bash: vol0001.nii.gz: command not found. Is there a way around this? The filenames need to be in string format to be fed into subsequent processing steps.

Thanks, David

Upvotes: 2

Views: 61

Answers (1)

xhienne
xhienne

Reputation: 6134

Use an array for this:

vol=()
for ((volume = 1; volume <= num_ap_files; volume++)); do
    bindex=$(sed -n "$volume p" ../b0_volumes_tmp.txt)
    vol[$volume]=$(sed -n "$bindex p" ../all_volumes.txt)
done

files="${vol[*]}"

The variable files contains the content of the array vol as one single string.

If you now want to call a command with each element of vol as an argument, no need to use an intermediate variable like files:

my_next_command "${vol[@]}"

Note: the command sed -n "$N p" file prints the Nth line of the file (the same as your cat file | head -$N | tail -1)

Upvotes: 2

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