Passing string argument from bash script to python3

Question

I am trying to read multiple directory locations from a text file using a bash script and pass as argument to another python script. The directory name contains space which shows

test.py: error: unrecognized arguments: 1B/PHASE/PHASE_90

I am using following bash script:

filename='filter_directory.txt'
line_counter=1
while read line; do
# reading each line
    echo "Processing Directorie: $line_counter : $line"
    python3 test.py -i $line
    line_counter=$((line_counter+1))
    echo "Finish Directorie: $line_counter!!!"
    done < $filename

test.py is:

import argparse
parser = argparse.ArgumentParser()
parser.add_argument("--input", "-i", type=str, default='./input', help='Calculation LUMA image folder')
arg = parser.parse_args()
input_path = arg.input
print(input_path)

filter_directory.txt contains:

version_of_study/Study 1B/PHASE/PHASE_90
version_of_study/Study 1B/PHASE/PHASE_91
version_of_study/Study 1B/PHASE/PHASE_92
version_of_study/Study 1B/PHASE/PHASE_93

Could you help me to import the directory name from text file to python by bash script?

Jedi · Accepted Answer · 2021-02-04 23:44:27Z

2

You should just quote $line like python3 test.py -i "$line" to group the argument. You can use tools like shellcheck to identify issues like these in shell scripts. This article is a great introduction to the different ways to correct use/avoid variable expansion and word splitting.

edited Feb 4, 2021 at 23:44

answered Feb 4, 2021 at 23:40

Jedi

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1 Comment

user4019417 Over a year ago

+1 for the shellcheck link. Genuinely needed a link to some form of shell debugging tool!! I find bug fixing bash like pulling teeth sometimes!!! I tend to resort to lots of echo statements and things like that!

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