Modern localization loaders (DeepLoc2/MULocDeep/COMPARTMENTS/UniProt); drop WoLF PSORT#667
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…rot); drop WoLF PSORT parseScores is rewritten to dispatch over modern sources: deeploc (default), cello (kept), mulocdeep (wide id+probabilities table), compartments (a COMPARTMENTS jensenlab.org channel TSV, aggregated per gene x compartment with a minConfidence filter), and uniprot (a UniProtKB 'Subcellular location [CC]' export). New defaultCompartmentMap (label -> model compartment id, with synonym merging) is accepted as 'compartmentMap' to rename/collapse compartments; new getUniProtScores fetches curated locations straight from the UniProt REST API by organism id (handles the gzip-compressed stream). WoLF PSORT is dropped entirely: getWoLFScores removed, parseScores 'wolf' now errors with guidance, and WoLFPSORT pulled from downloadRavenBinaries, the offline-bundle assembler, software/versions.txt, CONTRIBUTING and test docs. tLocalization is rewritten with real fixture-driven tests (8, all passing in MATLAB) covering every source plus two regression tests for UniProt parsing (whole-word matching so 'Cytoplasmic vesicle' is not mis-read as cytosol; per-isoform Note= stripping so later-isoform locations survive). predictLocalization's defaultCompartment error now lists the valid compartments. getUniProtScores validated live against UniProt (CIT1 -> YNR001C -> mitochondrion). doc/ is left to the release-time updateDocumentation regen.
Function test results240 tests 218 ✅ 1m 3s ⏱️ Results for commit 14de470. |
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Modern subcellular-localization loaders; drop WoLF PSORT
Mirrors the raven-toolbox change: replaces the single-label WoLF PSORT caller with modern multi-label predictors and curated evidence databases for
predictLocalization.parseScoresrewritten (name-value args; defaultdeeploc)Dispatches over
predictor:deeploc(default) — DeepLoc 2 per-protein CSV (kept)cello— CELLO (kept)mulocdeep— MULocDeep wide table (gene id + one probability column per compartment)compartments— a COMPARTMENTS channel TSV (e.g.yeast_compartment_integrated_full.tsvfrom download.jensenlab.org), aggregated per gene×compartment with aminConfidencefilteruniprot— a UniProtKBSubcellular location [CC]TSV exportPlus
compartmentMap+ newdefaultCompartmentMap(predictor/DB label → model compartment id, merging synonyms by max), so labels line up with the model's compartment ids, andidColumnformulocdeep/uniprot.New
getUniProtScoresFetches curated locations directly from the UniProt REST API by organism id (e.g.
getUniProtScores(559292)), handling the gzip-compressed/streamresponse.idFielddefaults to the ordered-locus ORF id so it matches yeast-GEM genes. Validated live (CIT1 → YNR001C → mitochondrion).WoLF PSORT dropped entirely
getWoLFScoresremoved;parseScores('...,'wolf')now errors with guidance; WoLFPSORT removed fromdownloadRavenBinaries, the offline-bundle assembler,software/versions.txt,tBinaries, CONTRIBUTING and the test README.Tests —
tLocalizationrewritten, 8 pass in MATLABFixture-driven coverage of every source +
defaultCompartmentMap, including two regression tests for the UniProt parser caught in pre-PR review:Cytoplasmic vesicleis not mis-coded as cytosol;Note=stripping so a later isoform's location survives.predictLocalization'sdefaultCompartmenterror now lists the valid compartments.Notes
doc/HTML is the release-timeupdateDocumentationsnapshot, so it is intentionally not regenerated here (the deleted page was restored to avoid dangling links until the next release regen).