I'm about to launch and perform an action in every subdir on one parent directory using this:

    for i in ./*/*R1.fastq;
do
    if [ -d "${i}" ]; then
        echo "${i}" 
        python2.7 demultadapt.py -f $i -p Demul-01-R1 FILE_ADAPT
    fi
done

but it never succeed. Please help!

CodePudding user response：

Please properly explain what you are trying to achieve.

Do you want to act on all directories that contain *R1.fastq files?

for f in ./*/*R1.fastq; do
    d=$(dirname "$f")
    if [ -d "$d" ]; then
        echo "$d" 
        python2.7 demultadapt.py -f "$d" -p Demul-01-R1 FILE_ADAPT
    fi
done

CodePudding user response：

Why not do this with find?

find <parent> -type d -print -exec python2.7 demultadapt.py -f {} -p Demul-01-R1 FILE_ADAPT \;

Where

• <parent> is your starting / parent directory
• -type d only return directories
• -print print out every hit
• -exec <command> \; in each directory execute your command. Note that {} will be replaced by the current hit, and the trailing \; is required.