Question

I am currently trying to write a script that will loop through multiple directories. The main raw_data directory contains ~150 subdirectories (subj001, subj002,…,subj00n), each of which has several subdirectories.

How can I make sure that the output from the script given bellow will be sent back to the specific subdirectory (e.g. subj0012) the input was taken from, rather than the current directory (raw_data)?

#!/bin/bash

for dir in ~raw_data/*
do
  tractor -d -r -b preproc RunStages:1 
done 

Thank you.

Answer 1

The name of the dir you want to save the output to is in $dir, right? So, just send the output there via redirection:

#!/bin/bash
for dir in ~raw_data/* ; do
    tractor -d -r- b preproc RunStages:1 > $dir/output
done

You should make sure that what you are processing really is a directory, though.