Use KEGG 118 HMM libraries in getKEGGModelForOrganism#642
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Point getKEGGModelForOrganism at the kegg118 pre-trained HMM sets published in the raven-toolbox v0.3.0 release. The recognised dataDir suffixes become euk90_kegg118 / prok90_kegg118, and the auto-download URL fetches kegg118_<domain>.hmm.gz from the v0.3.0 release (previously kegg116 from v0.1.0). Only the two kegg118 HMM sets (eukaryotes, prokaryotes) are supported; earlier KEGG releases are no longer offered for download. Update the tutorial5 example to use euk90_kegg118 accordingly.
Function test results202 tests 178 ✅ 33s ⏱️ Results for commit db21ef4. ♻️ This comment has been updated with latest results. |
getKEGGModelForOrganism recognised dataDir suffixes euk90_kegg118 / prok90_kegg118 but built the download URL from a second, index-aligned array (eukaryotes / prokaryotes), and the published asset is named differently again (kegg118_eukaryotes). Three names for one artefact. Standardise on the published asset name: dataDir is now kegg118_eukaryotes / kegg118_prokaryotes, so the local directory, the local .hmm library, and the downloaded asset all share one name. The hmmDomains/hmmIndex parallel array is removed -- the matched dataDir suffix doubles as the download filename. Docstring and the tutorial5 example updated accordingly.
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Summary
Switches
getKEGGModelForOrganismto the KEGG 118 pre-trained HMM sets published in the raven-toolboxv0.3.0release, and unifies the naming of those sets.KEGG 118 support
…/releases/download/v0.3.0/(previously kegg116 fromv0.1.0).Naming clean-up
Previously there were three names for one artefact: the recognised
dataDirsuffix (euk90_kegg118), an internal index-aligned array used only to build the URL (eukaryotes), and the published asset itself (kegg118_eukaryotes).dataDiris now styledkegg118_eukaryotes/kegg118_prokaryotes— identical to the published asset, so the local directory, the local.hmmlibrary, and the downloaded file all share one name.hmmDomains/hmmIndexparallel array is removed; the matcheddataDirsuffix doubles as the download filename.tutorial5example updated (the latter also moved off the long-staleeuk90_kegg105).This matches raven-toolbox, which already names the libraries
kegg<version>_<domain>.Notes
v0.3.0release (companion PR: Prepare kegg118 KEGG release (v0.3.0) raven-toolbox#41).doc/HTML still shows the old strings; it is produced byinstallation/updateDocumentation.m(m2html) and should be regenerated by a maintainer with MATLAB rather than hand-edited.Testing
assumeFail(require a local KEGG dump and external aligners), so they were not exercised here. Changes are string/URL/control-flow updates verified by inspection.