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I’m trying to loop a python script in bash that gets stats from fastq files. I want it to loop through all the fastq files in a directory and save the outputs in a text file. Ideally don’t want to edit the python script
This is the script that works when I’m not looping it:
python pythonscript.py -i fastqfile1.fq -q > stats1.txt
This is the loop that doesn’t work for me:
for f in *.fq; do python pythonscript.py -i "$f" -q; do echo "${f%.*}" > "stats${f%.fq}.txt" done
Thank you
EDIT I have put the loop in a bash .sh script. The error message I get is ” looping_script.sh: line 5: syntax error near unexpected token do' looping_script.sh: line 5:
do’ “
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Answer
Like this if you want all results in a single file:
for f in *.fq; do python pythonscript.py -i "$f" -q done > results.txt