From your question, we can't say much about your fasta headers and how you should transform them.

For example, your could use sed with option -f script-file

$ cat change.sed
s/^>ABCD/>EFG/
s/^>ID1/>sequence_1/
s/^>id\([A-Z]*\)/>sequence_\1/

$ for F in OLD*.fasta; do sed -f change.sed $F >  NEW/`basename $F` ; done

Thanks a lot Pierre. I did what you wrote and that worked well.

I would like to remind the beginners like me that NEW in the command line is a folder name we need to make in the same working directory.

Best

Hossein