Resolved: Bash loop on files in folder without specific pattern

Question:

I have to cycle over the files present in a folder but I dont want to cycle over files with a specific pattern (“Reverse”). Here is the code
Thanks

DIRECTORY=/Users/Qi.Wang/projects/CH12F3/data/CH12F3.LAM-HTGTS_mMYC.220512
outputDir=/Users/Qi.Wang/projects/CH12F3/
pw=$(pwd)
cat blank.txt > ./config.txt
c="$pw/config.txt"
o=0
for i in $DIRECTORY/*.fna; do
    ((o=o+1))
    s=${i##*/}
    b=${s%.fna}
    b="${o}_$(echo $b | awk '{ gsub(/_PairEnd+/, " " ); print $1 }')"
    outputDirs="$outputDir$b"
    printf "%s\t" $b >> ./config.txt
    printf "%s\t" $s >> ./config.txt
    cat end.txt >> ./config.txt
    printf "perl /Users/andy/projects/HTGTS/pipeline/align_tools/TLPpipeline.pl %s %s which=%s assembly=mm9 blatopt=mask=lower outdir=/%s -skipred -skipredadd -skipblu -skipbluadd \n" $c $DIRECTORY $o  $outputDirs >> ./command.sh
done

I Also have another minor problem. When i printf outdirs=%s the variable that is printed is $outputDir that starts with a “/” but after it got printed by printf, looks like the / is not there anymore.

Answer:

Your awk command puts spaces $b, so $outputDirs will contain spaces. Therefore, you need to quote it to make it a single argument to printf. You should also quote all the other variable arguments.
Also, since you’re creating a perl command line, you’ll want outdir=%s to be a single argument, so you should put single quotes around that as well.

printf "perl /Users/andy/projects/HTGTS/pipeline/align_tools/TLPpipeline.pl '%s' '%s' 'which=%s' assembly=mm9 blatopt=mask=lower 'outdir=/%s' -skipred -skipredadd -skipblu -skipbluadd \n" "$c" "$DIRECTORY" "$o"  "$outputDirs" >> ./command.sh

To skip files with Reverse in the name, enable extended globbing and use a non-matching pattern.

shopt -s extglob

for i in "$DIRECTORY"/!(*Reverse*).fna; do

If you have better answer, please add a comment about this, thank you!

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