Updating problematic positions to be more flexible

[evelyn-schmidt]

try to match pvacseq code

  --problematic-amino-acids PROBLEMATIC_AMINO_ACIDS
                        A list of amino acids to consider as problematic. Each
                        entry can be specified in the following format:
                        `amino_acid(s)`: One or more one-letter amino acid
                        codes. Any occurrence of this amino acid string,
                        regardless of the position in the epitope, is
                        problematic. When specifying more than one amino acid,
                        they will need to occur together in the specified
                        order. `amino_acid:position`: A one letter amino acid
                        code, followed by a colon separator, followed by a
                        positive integer position (one-based). The occurrence
                        of this amino acid at the position specified is
                        problematic., E.g. G:2 would check for a Glycine at
                        the second position of the epitope. The N-terminus is
                        defined as position 1. `amino_acid:-position`: A one
                        letter amino acid code, followed by a colon separator,
                        followed by a negative integer position. The
                        occurrence of this amino acid at the specified
                        position from the end of the epitope is problematic.
                        E.g., G:-3 would check for a Glycine at the third
                        position from the end of the epitope. The C-terminus
                        is defined as position -1. (default: None)