From 8af0d325bac20abcd8c1fd9e5ba511a2d9dd90ca Mon Sep 17 00:00:00 2001 From: Eduard Kerkhoven Date: Tue, 3 Nov 2026 09:33:06 +0100 Subject: [PATCH] Update the KEGG assets to kegg120 KEGG_VERSION.md names the kegg120 release, and fetchToolboxAsset reads the manifest manifest-v4. --- CHANGELOG.md | 6 ++++++ src/installation/fetchToolboxAsset.m | 8 ++++---- src/reconstruction/kegg/KEGG_VERSION.md | 2 +- src/reconstruction/kegg/getKEGGModelForOrganism.m | 6 +++--- src/reconstruction/kegg/keggDataVersion.m | 2 +- src/reconstruction/kegg/readKEGGTable.m | 2 +- tutorials/tutorial5.m | 4 ++-- 7 files changed, 18 insertions(+), 12 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 423aec56..a26fcd31 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,11 @@ # Changelog +## Unreleased + +### Data + +* The KEGG assets are the `kegg120` release of `toolbox-assets` (was: `kegg118`), and `fetchToolboxAsset` reads the manifest `manifest-v4`. + ## 3.0.0b2 — 2026-11-01 Second beta toward 3.0. Changes below are relative to 3.0.0b1. diff --git a/src/installation/fetchToolboxAsset.m b/src/installation/fetchToolboxAsset.m index cbd3b0bf..ea550544 100644 --- a/src/installation/fetchToolboxAsset.m +++ b/src/installation/fetchToolboxAsset.m @@ -9,7 +9,7 @@ % supplies the release tag and the asset name. % % A download is checked against the SHA-256 checksum that the -% toolbox-assets manifest (release manifest-v3) lists for it. A file whose +% toolbox-assets manifest (release manifest-v4) lists for it. A file whose % checksum differs is deleted and an error is raised. An asset that the % manifest does not list, or a manifest that cannot be read, gives a % warning and the file is kept unchecked. @@ -19,9 +19,9 @@ % destDir : char % directory to download into (created if it does not exist yet). % releaseTag : char -% the toolbox-assets release tag, for example 'kegg118'. +% the toolbox-assets release tag, for example 'kegg120'. % assetName : char -% the release asset file name, for example 'kegg118_core.tar.gz'. +% the release asset file name, for example 'kegg120_core.tar.gz'. % % Returns % ------- @@ -75,7 +75,7 @@ sha=''; if isempty(manifest) try - manifest=webread('https://github.com/CompMetEng/toolbox-assets/releases/download/manifest-v3/manifest.json', ... + manifest=webread('https://github.com/CompMetEng/toolbox-assets/releases/download/manifest-v4/manifest.json', ... weboptions('ContentType','json','Timeout',30)); catch ME warning('RAVEN:fetchToolboxAsset:manifest','Cannot read the toolbox-assets manifest: %s',ME.message); diff --git a/src/reconstruction/kegg/KEGG_VERSION.md b/src/reconstruction/kegg/KEGG_VERSION.md index e43f3b80..f86f3697 100644 --- a/src/reconstruction/kegg/KEGG_VERSION.md +++ b/src/reconstruction/kegg/KEGG_VERSION.md @@ -1,4 +1,4 @@ -kegg118 +kegg120 This is the toolbox-assets release tag that every KEGG-artefact download in this folder reads from --- getModelFromKEGG's core reference-model/table diff --git a/src/reconstruction/kegg/getKEGGModelForOrganism.m b/src/reconstruction/kegg/getKEGGModelForOrganism.m index 319e7a72..395bd6e1 100755 --- a/src/reconstruction/kegg/getKEGGModelForOrganism.m +++ b/src/reconstruction/kegg/getKEGGModelForOrganism.m @@ -26,8 +26,8 @@ % case, cutOff, minScoreRatioKO, minScoreRatioG and dataDir are not % used (default []). % dataDir : char -% directory of the HMM library, named kegg118_prokaryotes or -% kegg118_eukaryotes. The name gives the KEGG version and whether the +% directory of the HMM library, named kegg120_prokaryotes or +% kegg120_eukaryotes. The name gives the KEGG version and whether the % HMMs were trained on pro- or eukaryotic sequences, and matches the % published HMM library it is paired with. The prebuilt concatenated KO % HMM library (dataDir.hmm) is downloaded from the corresponding @@ -96,7 +96,7 @@ % 2. From protein homology (fastaFile supplied). The query proteome is % searched, in a single hmmsearch, against a prebuilt KEGG-version- and % domain-specific concatenated KO HMM library (for example -% kegg118_eukaryotes), downloaded from the corresponding toolbox-assets +% kegg120_eukaryotes), downloaded from the corresponding toolbox-assets % release if not already present in dataDir. Hits are filtered by cutOff, % minScoreRatioKO and minScoreRatioG into a KO-gene matrix, from which the % model is built (spontaneous reactions without genes are kept if diff --git a/src/reconstruction/kegg/keggDataVersion.m b/src/reconstruction/kegg/keggDataVersion.m index c8ee5493..93765ef6 100644 --- a/src/reconstruction/kegg/keggDataVersion.m +++ b/src/reconstruction/kegg/keggDataVersion.m @@ -9,7 +9,7 @@ % Returns % ------- % version : char -% the toolbox-assets release tag, for example 'kegg118'. +% the toolbox-assets release tag, for example 'kegg120'. ravenPath=findRAVENroot(); versionFile=fullfile(ravenPath,'src','reconstruction','kegg','KEGG_VERSION.md'); diff --git a/src/reconstruction/kegg/readKEGGTable.m b/src/reconstruction/kegg/readKEGGTable.m index 76ebe6e7..e04a21ec 100644 --- a/src/reconstruction/kegg/readKEGGTable.m +++ b/src/reconstruction/kegg/readKEGGTable.m @@ -7,7 +7,7 @@ % Parameters % ---------- % gzFile : char -% path to the gzipped TSV file, for example '.../kegg118_ko_reaction.tsv.gz'. +% path to the gzipped TSV file, for example '.../kegg120_ko_reaction.tsv.gz'. % % Returns % ------- diff --git a/tutorials/tutorial5.m b/tutorials/tutorial5.m index 5f1a985d..fec93652 100755 --- a/tutorials/tutorial5.m +++ b/tutorials/tutorial5.m @@ -10,7 +10,7 @@ % % Start by downloading trained Hidden Markov Models for eukaryotes. This can % be done automatically or manually from the RAVEN Wiki in its GitHub -% repository. In this tutorial, the archive "kegg118_eukaryotes" is picked for +% repository. In this tutorial, the archive "kegg120_eukaryotes" is picked for % the automatic download. See the documentation in the RAVEN Wiki for more % information regarding preparation of such archive. % @@ -20,7 +20,7 @@ % are for. This process takes up to 20-35 minutes in macOS, Unix systems and % 40-55 minutes in Windows, depending on your hardware and the size of % target organism proteome -model=getKEGGModelForOrganism('sce','sce.fa','kegg118_eukaryotes','output',false,false,false,false,10^-30,0.8,0.3,-1); +model=getKEGGModelForOrganism('sce','sce.fa','kegg120_eukaryotes','output',false,false,false,false,10^-30,0.8,0.3,-1); % The resulting model should contain around 1589 reactions, 1600 % metabolites and 836 genes. Small variations are possible since it is an