If you already have Seq IDs that should be deleted from the original file, you can do what @Ram suggested(creating subset from large file) with following oneliners

grep '^>' original_fasta.fa > original_ids.txt
grep -F -x -v -f ids_to_delete.txt original_ids.txt > ids_to_keep.txt

With the ids in ids_to_keep.txt file, you can extract the subset of sequences with faSomeRecords, take a look at the following link

A: perl code to extract sequences from multi-line fasta works on all test files but

Why do you wish to delete content from a file? From what I can guess, you either wish to extract a subset from a larger file or split the larger file into smaller files.

Also, the script above looks like it extracts sequence by ID to a new file - the ${line} is the variable containing the ID of the sequence. Therefore, loops would only work if you have a set of IDs the variable can iterate over.

You can use the --invert-match option with pyfaidx and a little bash:

$ pip install pyfaidx
$ faidx -v big.fasta $(tr '\n' ' ' < ids_to_remove.txt) > smaller.fasta