How to extract filename without extension and change header in the same file with the extracted name?

Question

I have about 30 VCF files with filenames as ID_001.new.vcf. I want to extract only the "ID_001" part from the filename and change it in the header line of the VCF file where "Sample1" is given:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Sample1

So that the result would look like:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  ID_001

How can I do it?

I have tried to use echo in bash and extract the IDs from the Filename but I am unable to iterate it to change inside the file.

Thanks for your help.

Answer 1

You could use the below :

for file in *.vcf 
do 
   name=$(basename -- "$file" .new.vcf) 
   sed -i "s/Sample1/$name/g" "$file" 
done