Case-sensitive separator filtering

[clonder]

Issue
In kinex.py:

if not phospho_priming:
    sequence = sequence.upper()

The sequence string is converted to uppercase, which affects any substrings used as separators. For example, (ph) becomes (PH).

In sequence.py:

class SequenceSeparator(Enum):
    ASTERISK = "*"
    PH = "(ph)"
    
valid_patterns = get_valid_patterns(separator)
if not any(pattern in sequence_string for pattern in valid_patterns):
    return False

The valid patterns, such as (ph) from SequenceSeparator, do not match the uppercase-transformed string, leading to invalid filtering.

Example:

• Original sequence: AAAAAAAGDS(ph)DSWDADAFSVEDPVR
• Separator: (ph)
• The sequence is transformed to uppercase, resulting in: AAAAAAAGDS(PH)DSWDADAFSVEDPVR.
• Separator should be (PH), but it is not in the list.

Proposed Fix

If it is a valide issue, I added uppercase separator in #6 pull request!