feat(speclib): Skyline transition list CSV support + speclib_build_cli bundle#55
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feat(speclib): Skyline transition list CSV support + speclib_build_cli bundle#55
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…r msgpack.zst Add pub constructors (new()) to PrecursorEntry, ReferenceEG, and SerSpeclibElement so external crates can construct speclib entries. Make PrecursorEntry pub. Add SpeclibWriter<W> wrapping zstd::Encoder for streaming msgpack.zst output. Re-export all four types from data_sources. Two roundtrip tests cover both rmp_serde encode/decode and the full writer→reader pipeline.
- clap CLI with all args + TOML config merge (CLI > TOML > defaults) - Proforma mod parser: fixed + variable mod application - Bloom + bucket HashMap peptide dedup - REVERSE + EDGE_MUTATE decoy strategies - Example config at repo root
- lib.rs re-exports for integration test access - 3 integration tests: digestion+dedup, mod chain, decoy roundtrip - Taskfile: speclib:build, speclib:local-koina, speclib:stop-koina
- Prosit expects bare AA sequences, strip bracket mods before sending - Convert Koina annotation format (y1+1) to mzPAF format (y1^1) - Make strip_mods pub for pipeline use
…warn affected proteins
- Precursor m/z now computed from modified sequence (includes +57 for Cys carbam) - Koina receives modified sequences with [UNIMOD:N] notation (Prosit handles them) - to_proforma converts [U:N] → [UNIMOD:N] (rustyms parses [U:N] as element Uranium) - Isotope distribution also uses modified formula
- Add Prosit_2023_intensity_timsTOF and Prosit_2020_intensity_CID to model registry - Default fragment model now timsTOF-specific (was HCD) - Same Triton v2 schema, drop-in compatible
- Tolerance::default() now uses RtTolerance::Unrestricted (was Minutes(5,5))
- Prescore extracts full RT range, calibration maps library→observed RT
- Bench config drops explicit RT tolerance (defaults to unrestricted)
- Users with calibrated libraries can still set "rt": {"minutes": [N, N]} in config
New skyline_io module parses Skyline Peptide Transition List exports as a spectral library source, mirroring the DIA-NN/Spectronaut pattern (sniff + group-by-precursor + emit TimsElutionGroup<IonAnnot> plus SkylinePrecursorExtras). Wires through timsquery's dispatch, timsquery_viewer's extras view, and timsseek's speclib converter (reusing convert_diann_to_query_item via a small extras adapter). Notable behaviors: - Precursor-isotope rows (Fragment Ion Type == "precursor") are skipped; downstream computes the envelope from the sequence. - `#N/A` Library Intensity values default to 1.0. - RT/IM columns are absent in Skyline exports; defaults to 0.0 with a loud warning (use Unrestricted RT tolerance). - Modifications in `[...]` are stripped for the stripped_peptide field; modified_peptide is preserved verbatim.
…d_cli Drops the Python speclib_builder package and all references (root pyproject workspace/deps, hatch packages, uv sources, uv.lock). The Rust speclib_build_cli now owns the digest → dedup → expand → Koina predict → write pipeline end-to-end.
No notebooks in the repo and no other references to jupyter. Prunes ~100 transitive deps from uv.lock.
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Summary
skyline_iomodule mirrors the DIA-NN/Spectronaut pattern (sniff + group-by-precursor →TimsElutionGroup<IonAnnot>+SkylinePrecursorExtras), wired through timsquery dispatch, timsquery_viewer extras, and timsseek speclib converter.main: thespeclib_build_cliRust CLI (digest → dedup → expand → Koina predict → write msgpack.zst), Prosit_2023_intensity_timsTOF default, iRT-library RT tolerance default (Unrestricted), and related fixes.Skyline specifics
Fragment Ion Type == "precursor") skipped; envelope computed from sequence downstream.#N/ALibrary Intensity → default 1.0.UnrestrictedRT tolerance).[...]stripped forstripped_peptide;modified_peptidepreserved verbatim.Test plan
cargo test -p timsquery --lib serde::— 19 tests pass (6 new skyline_io tests)cargo test -p timsseek --lib speclib— 12 tests pass (test_load_skyline_csv_librarynew)cargo build -p timsquery -p timsseek -p timsquery_viewerclean