[SOLVED] remove characters from filename in bash

Issue

I am trying to remove specific characters from a file in bash but am not getting the desired result.

bash

for file in /home/cmccabe/Desktop/NGS/API/test/*.vcf.gz; do
mv -- "$file" "${file%%/*_variants_}.vcf.gz"
done

file name

TSVC_variants_IonXpress_004.vcf.gz

desired resuult

IonXpress_004.vcf.gz

current result (extention in filename repeats)

TSVC_variants_IonXpress_004.vcf.gz.vcf.gz

I have tried to move the * to the end and to use /_variants_/ and the same results. Thank you :).

Solution

${var%%*foo} removes a string ending with foo from the end of the value of var. If there isn't a suffix which matches, nothing is removed. I'm guessing you want ${var##*foo} to trim from the beginning, up through foo. You'll have to add the directory path back separately if you remove it, of course.

mv -- "$file" "/home/cmccabe/Desktop/NGS/API/test/${file##*_variants_}"

Answered By - tripleee

Answer Checked By - Mary Flores (WPSolving Volunteer)