[BUG] Fix clean_protein_seq corrupting lowercase sequences (#348)

[Alleny244]

Reference Issues/PRs

Fixes: #550

What does this implement/fix? Explain your changes.

clean_protein_seq() in pyaptamer/utils/_pseaac_utils.py only validates against
uppercase AMINO_ACIDS, so lowercase input like "acdef" is incorrectly replaced
with "NNNNN". Added seq = seq.upper() at the start of the function to normalize
input before validation.

What should a reviewer concentrate their feedback on?

• Whether upper() is the right normalization strategy (vs. checking both cases)
• Whether the test cases sufficiently cover edge cases

Did you add any tests for the change?

Yes — added parametrized tests in pyaptamer/pseaac/tests/test_pseaac.py:

• Fully lowercase sequence input
• Mixed-case sequence input

Both verify that the cleaned output matches seq.upper().

Any other comments?

None

PR checklist

• The PR title starts with either [ENH], [MNT], [DOC], or [BUG]. [BUG] - bugfix, [MNT] - CI, test framework, [ENH] - adding or improving code, [DOC] - writing or improving documentation or docstrings.
• Added/modified tests
• Used pre-commit hooks when committing to ensure that code is compliant with hooks. Install hooks with pre-commit install.
  To run hooks independent of commit, execute pre-commit run --all-files