feat: add ClustalW .aln format support for sequence alignments

[haoyu-haoyu]

Summary

Add support for reading and writing ClustalW .aln alignment files, following the existing FASTA alignment I/O pattern.

New files

File	Description
src/biotite/sequence/io/clustal/__init__.py	Package exports
src/biotite/sequence/io/clustal/file.py	ClustalFile class (TextFile + MutableMapping)
src/biotite/sequence/io/clustal/convert.py	get_alignment() / set_alignment() conversion functions
tests/sequence/data/clustal.aln	Single-block test data
tests/sequence/data/clustal_multi.aln	Multi-block test data
tests/sequence/test_clustal.py	9 test cases

Implementation details

ClustalFile

• Extends TextFile and MutableMapping (same pattern as FastaFile)
• Parses CLUSTAL header, sequence blocks, and consensus lines
• Dict-like interface: clustal_file["seq1"] returns gapped sequence string
• Handles multi-block alignments by concatenating segments per sequence name

Conversion functions

• get_alignment(clustal_file, seq_type=None) — auto-detects nucleotide/protein
• set_alignment(clustal_file, alignment, seq_names, line_length=60) — formats into blocks

Edge cases handled

• Empty file → InvalidFileError
• Missing CLUSTAL header → InvalidFileError
• Single sequence → clear ValueError (alignments need ≥ 2 sequences)
• line_length=0 → ValueError
• Reusing a ClustalFile object → entries cleared before writing
• Consensus lines (with *, :, .) correctly skipped during parsing

Tests

9 tests covering: file reading, multi-block parsing, dict interface, alignment conversion, round-trip consistency (object-level and file I/O-level), name count mismatch error, and explicit sequence type parameter.

Closes #774

[padix-key]

Thanks for adding the parser 👍. I'll have a look 👀

[codspeed-hq]

Merging this PR will not alter performance

✅ 98 untouched benchmarks

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_{Comparing haoyu-haoyu:feat/clustalw-aln-format (83b69f9) with main (00d5b98)}