ALSO REQUIRE A MAN PAGE FOR THE TASK

This is not a code writing site. Nor is it a documentation writing site. We won't be keeping your job or finishing your studies. You have to do this yourself.

Your program looks very much like it is processing FASTA sequences. There are readymade modules for that. See FASTA or FASTA on this site.

Update: If this is a university assignment, most likely your course materials cover how to find the locations that cause the warnings and how to fix them. I recommend going over your course notes again.