Exhaustive list of everything gapsmith implements, one row per feature,
with pointers to both the upstream R source and the Rust module.
Status legend:
- ✅ — implemented and tested against real gapseq where feasible
- 🆕 — Rust-only feature (no upstream equivalent)
- ⚠️ — shipped but intentionally deviates from upstream (see porting-notes.md)
- ❌ — deferred / intentionally not ported
| Subcommand | R source | Rust module | Status |
|---|
gapsmith test | — | gapsmith-cli/src/commands/test.rs | ✅ |
gapsmith find | src/gapseq_find.sh + src/*.R | gapsmith-find/ + gapsmith-cli/src/commands/find.rs | ✅ byte-identical on PWY-6587 & amino |
gapsmith find-transport | src/transporter.sh + src/analyse_alignments_transport.R | gapsmith-transport/ + gapsmith-cli/src/commands/find_transport.rs | ✅ TC-set + row-count identical |
gapsmith draft | src/generate_GSdraft.R + src/prepare_candidate_reaction_tables.R | gapsmith-draft/ + gapsmith-cli/src/commands/draft.rs | ✅ SBML validates (0 libSBML errors) |
gapsmith medium | src/predict_medium.R | gapsmith-medium/ + gapsmith-cli/src/commands/medium.rs | ✅ byte-identical on ecoli |
gapsmith fill | src/gf.suite.R + src/gapfill4.R | gapsmith-fill/ + gapsmith-cli/src/commands/fill.rs | ✅ 4-phase suite + KO loop |
gapsmith adapt | src/adapt.R + src/gf.adapt.R | gapsmith-cli/src/commands/adapt.rs | ⚠️ EC / KEGG / name resolution deferred |
gapsmith pan | src/pan-draft.R | gapsmith-cli/src/commands/pan.rs | ✅ union + binary table |
gapsmith doall | src/doall.sh | gapsmith-cli/src/commands/doall.rs | ✅ end-to-end on ecore in 2m47s |
gapsmith update-sequences | src/update_sequences.sh | gapsmith-cli/src/commands/update_sequences.rs | ✅ Zenodo sync + md5 diff |
gapsmith convert | — | gapsmith-cli/src/commands/convert.rs | 🆕 CBOR ↔ JSON round-trip |
gapsmith example-model | — | gapsmith-cli/src/commands/example_model.rs | 🆕 toy model fixture |
gapsmith db inspect | — | gapsmith-cli/src/commands/db.rs | 🆕 reference-data row-count dump |
gapsmith export-sbml | cobrar::writeSBMLmod | gapsmith-cli/src/commands/export_sbml.rs | 🆕 CBOR → SBML |
gapsmith align | — | gapsmith-cli/src/commands/align.rs | 🆕 debug-wrap for a single aligner |
gapsmith batch-align | — | gapsmith-cli/src/commands/batch_align.rs | 🆕 cluster N genomes + single alignment |
gapsmith doall-batch | — | gapsmith-cli/src/commands/doall_batch.rs | 🆕 rayon + SLURM-shard parallel doall across N genomes |
gapsmith community per-mag | — | gapsmith-cli/src/commands/community.rs | 🆕 per-MAG FBA under a shared (union) medium |
gapsmith community cfba | — | gapsmith-cli/src/commands/community.rs | 🆕 compose N drafts, weighted-sum biomass objective |
gapsmith fba | — | gapsmith-cli/src/commands/fba.rs | 🆕 FBA / pFBA standalone |
| Feature | R source | Rust module |
|---|
| BLASTp wrapper | gapseq_find.sh blastp block | blast.rs::BlastpAligner |
| tBLASTn wrapper | same, for -n nucl | blast.rs::TblastnAligner |
| DIAMOND wrapper | gapseq_find.sh diamond block | diamond.rs::DiamondAligner |
| mmseqs2 wrapper (full pipeline) | gapseq_find.sh mmseqs block | mmseqs2.rs::Mmseqs2Aligner |
| Precomputed TSV input | — | precomputed.rs::PrecomputedTsvAligner 🆕 |
| Batch-cluster (N genomes → 1 alignment) | — | batch.rs::BatchClusterAligner 🆕 |
| gspa-run manifest reader (cluster-aware hit expansion) | — | gspa.rs::{GspaManifest, GspaRunAligner} 🆕 |
| 2-decimal scientific e-value format | BLAST -outfmt 6 native | tsv.rs |
| Feature | R source | Rust module |
|---|
| Pathway table loader (meta / kegg / seed / custom) | gapseq_find.sh:520-532 | gapsmith-db::PathwayTable |
| metacyc + custom merge (custom-wins-on-id) | same | same |
Keyword-shorthand resolution (amino, carbo, ...) | gapseq_find.sh:40-60 | pathways.rs::MatchMode::Hierarchy |
Reference FASTA resolver (user/ → rxn/ → rev/EC → unrev/EC → md5) | prepare_batch_alignments.R:150-234 | seqfile.rs |
| Complex-subunit detection | complex_detection.R | complex.rs (R-parity on 9 cases) |
| Hit classification with exception table | analyse_alignments.R:108-189 | classify.rs |
Pathway completeness scoring (f64 precision) | filter_pathways.R:10-34 | pathways.rs::score |
dbhit lookup (EC + altEC + MetaCyc id + enzyme name) | getDBhit.R:60-130 | dbhit.rs |
noSuperpathways=true default | gapseq_find.sh:20 | find::FindOptions |
Word-boundary-less header filter (matches shell grep -Fivf) | gapseq_find.sh | seqfile.rs ⚠️ intentional |
Output writers (Reactions.tbl, Pathways.tbl) | same | output.rs |
| Feature | R source | Rust module |
|---|
subex.tbl substrate filter | transporter.sh:140-280 | filter.rs |
| TC-id parsing + type canonicalisation | analyse_alignments_transport.R:1-188 | tc.rs |
| Substrate resolution (tcdb_all + FASTA header fallback) | same | runner.rs |
Alt-transporter reaction assignment (gated by --nouse-alternatives) | analyse_alignments_transport.R:110-130 | runner.rs |
Substrate-case preservation (gapseq emits sub=Potassium) | shell behaviour | data.rs |
| Feature | R source | Rust module |
|---|
| Candidate selection (bitscore ≥ cutoff OR pathway support) | prepare_candidate_reaction_tables.R + generate_GSdraft.R:55-100 | candidate.rs |
| Stoichiometric hash dedup | generate_rxn_stoich_hash.R | stoich_hash.rs |
Best-status-across-rows (OR is_complex, max complex_status, highest-rank pathway_status) | implicit in R's data.table merges | candidate.rs::build_candidates ⚠️ explicit |
| Biomass JSON parser (single + pipe-separated multi-link) | parse_BMjson.R:1-107 | biomass.rs + gapsmith-db::BiomassComponent::links |
| Biomass cofactor mass-rescaling | generate_GSdraft.R:281-292 | biomass.rs ⚠️ menaquinone-8 auto-removal deferred |
| GPR composition (and / or tree, "subunit undefined" edge cases) | get_gene_logic_string.R | gpr.rs |
| Diffusion + exchange expansion | add_missing_exRxns.R:1-156 | exchanges.rs |
| Conditional transporter additions (butyrate, IPA, PPA, phloretate) | generate_GSdraft.R | runner.rs::add_conditional_transporters |
SBML ID sanitiser (-/./:/space → _) | — | builder.rs 🆕 |
Cytosolic met-id format (cpd00001_c0 not cpd00001[c0]) | — | builder.rs ⚠️ for SBML SId compliance |
| Feature | R source | Rust module |
|---|
Split-flux LP encoding (vp, vn ≥ 0) | implicit in cobrar::pfbaHeuristic | lp.rs::SplitFluxLp |
| FBA | cobrar::fba | fba.rs::fba |
| pFBA (single call) | cobrar::pfbaHeuristic | pfba.rs::pfba |
pFBA-heuristic tolerance ladder (15 iters, 1e-6 → 1e-9, pFBA-coef relaxation) | gapfill4.R:95-137 | pfba.rs::pfba_heuristic |
| HiGHS solver | — (R uses glpk/cplex) | good_lp 1.15 + highs-sys |
| CBC fallback | — | pfba.rs::pfba_cbc (feature-gated cbc) 🆕 |
Row-expression builder (O(nnz)) | implicit | fba.rs::build_row_exprs 🆕 performance |
| Feature | R source | Rust module |
|---|
gapfill4 single-iteration driver | gapfill4.R:1-303 | gapfill.rs::gapfill4 |
Candidate pool (draft + all approved SEED, stoich-hash deduped) | construct_full_model.R + gapfill4.R:12-56 | pool.rs::build_full_model |
rxnWeights derivation from bitscores | prepare_candidate_reaction_tables.R:222-228 | pool.rs::rxn_weight |
| KO essentiality loop (serial, core-first, highest-weight-first) | gapfill4.R:247-280 | gapfill.rs::gapfill4 |
| Medium application (close all EX, open per-medium, add missing EX) | constrain.model.R | medium.rs::apply_medium |
Environment overrides (env_highH2.tsv) | adjust_model_env.R | medium.rs::apply_environment_file |
| Step 1 (user medium + biomass target) | gf.suite.R:244-258 | suite.rs::run_suite |
| Step 2 (per-biomass-component on MM_glu + carbon sources) | gf.suite.R:285-372 | suite.rs::step2 |
| Step 2b (aerobic / anaerobic variant) | gf.suite.R:377-464 | suite.rs::run_suite |
| Step 3 (energy-source screen with ESP1-5) | gf.suite.R:480-581 | suite.rs::step3 |
| Step 4 (fermentation-product screen) | gf.suite.R:585-683 | suite.rs::step4 |
| Target-met sink as objective | add_met_sink in add_missing_exRxns.R:56-72 | suite.rs::add_target_sink_obj |
| Futile-cycle detector (parallel pairwise LP probe) | recent upstream cccbb6f0 | futile.rs::detect_futile_cycles (opt-in --prune-futile) |
Community model composition (block-diagonal, shared _e0) | — | community.rs::compose_models 🆕 |
| Weighted-sum community biomass + optional balanced-growth | — | community.rs::add_community_biomass 🆕 |
Union-medium + per-MAG weights (community per-mag mode) | — | community.rs::{union_medium, per_mag_weights, weighted_growth} 🆕 |
| Feature | R source | Rust module |
|---|
| Rules-table loader | predict_medium.R:46 | rules.rs::load_rules |
Boolean-expression evaluator (| & ! < > == <= >=) | eval(parse(text=)) | boolexpr.rs::eval |
Counting-rule support (a + b + c < 3) | same (R int arithmetic) | boolexpr.rs::parse_sum |
| Cross-rule dedup + mean flux | predict_medium.R:84-86 | predict.rs::predict_medium |
| Saccharides / Organic acids category dedup | predict_medium.R:88-92 | predict.rs::predict_medium |
| Manual flux overrides | predict_medium.R:94-114 | predict.rs::parse_manual_flux |
| Proton balancer | predict_medium.R:121-132 | predict.rs::predict_medium |
| Feature | R source | Rust module |
|---|
| CBOR round-trip | — | gapsmith-io::{read,write}_model_cbor 🆕 |
| JSON round-trip | — | gapsmith-io::{read,write}_model_json 🆕 |
| SBML L3V1 + FBC2 + groups writer | cobrar::writeSBMLmod | gapsmith-sbml::write_sbml |
| SBML SId idempotent on mets with compartment suffix | — | writer.rs::species_id 🆕 bugfix |
Streaming via quick-xml | — | writer.rs 🆕 no libSBML dep |
| SBML consistency validation | libSBML native | tools/validate_sbml.py (libSBML + COBRApy) |
| Feature | R source | Rust module |
|---|
seed_reactions_corrected.tsv | data.table::fread | seed.rs::load_seed_reactions |
seed_metabolites_edited.tsv | same | seed.rs::load_seed_metabolites |
MNXref cross-refs (mnxref_*.tsv) | same | mnxref.rs |
meta_pwy.tbl / kegg_pwy.tbl / seed_pwy.tbl / custom_pwy.tbl | same | pathway.rs |
subex.tbl | same | subex.rs |
tcdb.tsv | same | tcdb.rs |
exception.tbl | same | exception.rs |
medium_prediction_rules.tsv | same | gapsmith-medium::rules |
complex_subunit_dict.tsv | same | complex.rs |
| Biomass JSON (Gram+, Gram-, archaea, user custom) | parse_BMjson.R | biomass.rs |
SEED stoichiometry parser (-1:cpd00001:0:0:"H2O";...) | parse_BMjson.R:21-29 | stoich_parse.rs |
| Feature | Rust module | Motivation |
|---|
Precomputed alignment input (--aligner precomputed -P <tsv>) | gapsmith-align::PrecomputedTsvAligner | Skip per-genome BLAST when the user pre-runs diamond / mmseqs2 at batch scale |
BatchClusterAligner (gapsmith batch-align) | gapsmith-align::BatchClusterAligner | Amortise alignment cost over N genomes via one mmseqs2 cluster + single alignment |
gspa-run manifest reader (--gspa-run <dir>) | gapsmith-align::GspaRunAligner | Consume precomputed cluster-rep hits from the upstream gspa pipeline; fans rep hits onto per-genome members |
gapsmith doall-batch | gapsmith-cli::commands::doall_batch | Rayon + SLURM-array-friendly driver for reconstructing 100 → 1 M genomes in one batch |
gapsmith community per-mag | gapsmith-fill::community + CLI | Shared-medium per-MAG FBA for metagenomes with 50+ MAGs |
gapsmith community cfba | gapsmith-fill::community + CLI | Full community LP (block-diagonal compose, weighted-sum biomass, optional balanced-growth) |
| In-process LP (HiGHS via good_lp) | gapsmith-fill | Replaces R cobrar's shelled-out glpk / cplex; faster warm-starts |
| Optional CBC fallback backend | gapsmith-fill::pfba_cbc (--features cbc) | When HiGHS exhausts the tolerance ladder on pathological LPs |
| CBOR native format | gapsmith-io | Fast, compact, stdlib-free; replaces R's RDS |
gapsmith fba subcommand | gapsmith-cli | Standalone FBA / pFBA without shelling into R |
gapsmith convert subcommand | gapsmith-cli | CBOR ↔ JSON round-trip for inspection |
gapsmith db inspect subcommand | gapsmith-cli | Smoke-test the reference data directory |
gapsmith export-sbml subcommand | gapsmith-cli | Write an arbitrary CBOR model as SBML |
| Gap | Upstream location | Workaround / plan |
|---|
| EC / TC conflict resolution (IRanges overlap math) | prepare_candidate_reaction_tables.R::resolve_common_{EC,TC}_conflicts | Affects <1 % of multi-EC annotations. Plan: port when a user case needs it. |
| MIRIAM cross-ref annotations (KEGG / BiGG / MetaNetX / HMDB / ChEBI) | addReactAttr.R + addMetAttr.R | SBML emits ModelSEED id only; round-trip in COBRApy still works. |
| HMM-based taxonomy / gram prediction | predict_domain.R, predict_gramstaining.R | CLI requires explicit `--taxonomy Bacteria |
| Gene-name MD5 fallback in seqfile resolver | uniprot.sh:179 | Common-case MD5 fallback is ported; gene-name branch rarely fires. |
| Menaquinone-8 auto-removal (gated on MENAQUINONESYN-PWY / PWY-5852 / PWY-5837) | generate_GSdraft.R:281-292 | Bio1 includes cpd15500 regardless; affects anaerobic predictions marginally. |
gram_by_network.R (predict gram by metabolic-network similarity) | same | Requires explicit `-b pos |
adapt EC / KEGG / enzyme-name resolution | adapt.R::ids2seed strategies 3–7 | Direct SEED + pathway id resolution works; user can pre-resolve via gapsmith find. |
pan weight medianing (custom_median) | pan-draft_functions.R | Pan-model emits without merged rxnWeights metadata; gapsmith fill on a pan-draft needs the source Reactions.tbl. |
| CPLEX solver support | — | Plan explicitly calls for HiGHS + optional CBC; no CPLEX path. |
MetaCyc DB updaters (meta2pwy.py, meta2genes.py, meta2rea.py) | upstream Python helpers | Run once per year by maintainers; kept in Python. |
| Test suite | Tests | What it asserts |
|---|
gapsmith-core unit | 18 | Type invariants, serde round-trips, stoichiometric matrix construction. |
gapsmith-io unit | 5 | CBOR / JSON round-trip, data-dir auto-detect. |
gapsmith-db unit | 18 | Every reference-data parser on realistic inputs. |
gapsmith-sbml unit + integration | 2 + 1 | SBML writer emits every FBC2 / groups element; libSBML validates cleanly. |
gapsmith-align unit + smoke + parity | 18 + 4 + 3 | Aligner trait, precomputed TSV, gspa-run manifest + fan-out, BLAST / diamond / mmseqs2 shell parity. |
gapsmith-find unit + smoke + parity | 36 + 1 + 2 | Pathway scoring, complex detection (R-parity on 9 cases), find -p PWY-6587 and -p amino byte-identical against real gapseq. |
gapsmith-transport unit + parity | 7 + 1 | TC parsing, substrate resolution, end-to-end row+TC-id parity against real gapseq. |
gapsmith-draft unit + smoke | 10 + 1 | Biomass rescaling, GPR composition, stoich dedup, conditional transporters. |
gapsmith-fill unit + textbook + smoke | 20 + 5 + 1 | FBA / pFBA / pFBA-heuristic on toys; community compose + cFBA on 2-organism toy; gapfill4 end-to-end on ecoli draft. |
gapsmith-medium unit | 14 | Boolean-expression evaluator (incl. counting rules), rule loader, cross-rule dedup, proton balance. |
gapsmith-cli integration | 6 + 1 | CBOR↔JSON round-trip end-to-end via the binary; SLURM-shard parser. |
| Total | ~170 | |
Run the full suite:
cargo test --workspace
cargo clippy --workspace --all-targets -- -D warnings
| Crate | src/ LOC | tests/ LOC |
|---|
gapsmith-core | ~1 000 | — |
gapsmith-io | ~330 | — |
gapsmith-db | ~1 600 | — |
gapsmith-sbml | ~870 | ~220 |
gapsmith-align | ~1 250 | ~560 |
gapsmith-find | ~2 700 | ~380 |
gapsmith-transport | ~1 040 | ~115 |
gapsmith-draft | ~1 670 | ~80 |
gapsmith-fill | ~2 150 | ~400 |
gapsmith-medium | ~550 | — |
gapsmith-cli | ~2 400 | ~60 |
| Total | ~17 000 | ~2 100 |