[padix-key]

For a profile with an RNA alphabet (A, C, G, U), SequenceProfile.to_consensus() always raised an AlphabetError: The consensus string was built with U, but the returned NucleotideSequence cannot encode U.

As NucleotideSequence represents both DNA and RNA and uses T for uracil, RNA profiles now use the same code path as DNA profiles, and the then unused _rna_to_consensus() is removed. The docstring mentions the T representation.

The existing nucleotide consensus tests are parametrized over the DNA and RNA alphabet. The new RNA cases fail without this fix.

Authored by Claude

[codspeed]

Merging this PR will regress 5 benchmarks

1 warning

⚠️ 9 benchmarks with a significant change ran on different hardware

Their base and head results were measured on machines with a different CPU, core count or memory, so the changes might not come from the code. Run base and head on the same runner type.

Learn more about Macro Runners

See affected benchmarks

⚡ 4 improved benchmarks
❌ 5 regressed benchmarks
✅ 102 untouched benchmarks
⏩ 14 skipped benchmarks¹

Warning

Please fix the performance issues or acknowledge them on CodSpeed.

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
❌	benchmark_match_kmer_selection[BucketKmerTable(10000)-None]	655.1 µs	770.7 µs	-15%
❌	benchmark_match[BucketKmerTable(10000)-None]	763.6 µs	880.4 µs	-13.26%
❌	benchmark_match[BucketKmerTable(10000)-11*11*1*1***111]	839.8 µs	959.4 µs	-12.47%
❌	benchmark_cell_list_compute_contacts[PAIRS]	22.6 ms	25.8 ms	-12.43%
❌	benchmark_cell_list_compute_contacts[MAPPING]	23.5 ms	26.7 ms	-12.01%
⚡	benchmark_structural_alphabet_methods[to_3di]	21.2 ms	14.1 ms	+50.24%
⚡	benchmark_superimpose[superimpose_structural_homologs]	45 ms	35.8 ms	+25.82%
⚡	benchmark_match_kmer_selection[KmerTable-11*11*1*1***111]	640.8 µs	521.9 µs	+22.79%
⚡	benchmark_match[KmerTable-11*11*1*1***111]	825.8 µs	709.1 µs	+16.45%

Tip

Investigate this regression by commenting @codspeedbot fix this regression on this PR, or directly use the CodSpeed MCP with your agent.

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_{Comparing padix-key:fix/profile-rna-consensus (cd2106b) with main (d46cc4e)²}

Footnotes

1. 14 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

2. No successful run was found on main (5eaa9e3) during the generation of this report, so d46cc4e was used instead as the comparison base. There might be some changes unrelated to this pull request in this report. ↩