feat(cluster): species-parameterize CORUM + MSigDB benchmark generation (#238) - #240
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…on (#238) Cluster benchmark generation hardwired human sources, so mouse (and other non-human) screens could not build the CORUM/KEGG group validators. - get_corum_data / generate_corum_group_benchmark: accept species_id; human keeps its native export unchanged, other species are filtered out of the CORUM complete export by organism. - generate_msigdb_group_benchmark: accept species_id and resolve the MSigDB collection per species (human=KEGG MEDICUS; mouse has no native KEGG, so the native mouse Reactome collection is used). Explicit url still overrides. - STRING and UniProt generators were already species-aware; no change. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01FRP7UVsNz6igHrJE72nVfT
This was referenced Jul 30, 2026
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Bring main (5 commits, #227/#231/#232/#234/#240) into the branch ahead of #171. Merged rather than rebased: a rebase replays 45 commits and re-hits the same aggregate collisions repeatedly, while the merge conflicts in one file, and main only accepts squash merges so the linear history would be flattened on landing anyway. Both conflicts are in generate_feature_table.py and are complementary: - #234 added a warning when perturbation_id_col is unset; the branch added the control_name_col fallback (#222). Independent, both kept. - Column ordering for the construct table: the branch dedupes via dict.fromkeys over [pert_id_col, pert_col, control_name_col, ...], main dedupes only the id/name pair. Kept the branch version -- main's drops control_name_col, which the control filter downstream indexes on, so main's form would KeyError under a construct-level config. ruff check and ruff format clean. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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Summary
Cluster benchmark generation (
workflow/lib/cluster/scrape_benchmarks.py) hardwired human sources, so mouse (and other non-human) screens could not build the CORUM/KEGG group validators. Closes #238.get_corum_data/generate_corum_group_benchmark): now acceptspecies_id. Human keeps its nativefile_id=humanexport unchanged (zero regression); other species are pulled from the CORUMcompleteexport and filtered by theorganismcolumn (CORUM has no per-organism download for them).generate_msigdb_group_benchmark): now acceptsspecies_idand resolves the collection per species. Human = KEGG MEDICUS (unchanged). Mouse has no native KEGG collection in MSigDB, so the native mouse Reactome collection is used. An expliciturlstill overrides.species_id-aware — no change; the companion analysis PR just starts passing them the species.Note on the mouse "KEGG" slot
For mouse, the second group validator is native Reactome data occupying the slot named
kegg_group_benchmark. This was a deliberate choice (native mouse pathways, no orthology inference) over orthology-converting human KEGG. Functionally it is a valid pathway group benchmark; the name is retained to avoid churn in config keys and downstream labels.Verification
Live smoke test (not covered by
small_test_analysis, which reads static committed TSVs and never invokes these generators):ruff check+ruff format --checkclean.