Filter out sequences that contain unknown amino acids

https://jira.gsc.wustl.edu/browse/AT-623
I decided to make a `sub valid_amino_acid_codes { keys %amino_acids }` and keep the rest of the functionality in the original RemoveUnknownSequences module. I thought that this was a good compromise since the rest is so specific to RemoveUnknownSequences. I will update this PR shortly with my change but I want to run test-tracker first and things are being slow.