Bash command that iterates throught folder and runs python script

Question

i am trying to run linux command to run python script:

for f in /mnt/data/service/fmriprep/geht/sub-P*; do (python 2_correlation.py -i "$f" -o /mnt/data/service/corr_graph/correlation_P*.csv ) 

my python script takes as input file in -i directory and return as -o a new .csv. I expect to return correlation_P* for each folder P* (P001, P002, P*) to this path (/mnt/data/service/corr_graph/correlation_P*.csv with the same P001,P002, P*), but stucked.

Answer 1

For each iteration of the loop, you need to extract the digits after "P" and use them in the csv file name:

in_dir=/mnt/data/service/fmriprep/geht out_dir=/mnt/data/service/corr_graph for dir in "$in_dir"/sub-P*; do num=${dir##*P} python 2_correlation.py -i "$dir" -o "$out_dir/correlation_P${num}.csv" done 

Answer 2

Great thanks to @glenn jackman, you raised my skill. So command which worked for me is:

for dir in /mnt/data/service/fmriprep/geht/sub-P*; do if [ -d "$dir" ]; then num=${dir##*P} && python 2_correlation.py -i "$dir" -o "/mnt/data/service/corr_graph/correlation_P${num}.csv";fi done