Skip to content

kegg: fetch the HMM library from the raven-data kegg118 release #643

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
edkerk merged 1 commit into from
Jun 16, 2026
Merged

kegg: fetch the HMM library from the raven-data kegg118 release #643

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
5 changes: 3 additions & 2 deletions reconstruction/kegg/getKEGGModelForOrganism.m
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -198,7 +198,8 @@
%pre-trained HMM set, compatible with the current RAVEN version. The
%reconstruction uses the concatenated KO HMM library (a single
%gzip-compressed flatfile, queried in one hmmsearch); if it is not already
%present it is downloaded from the corresponding RAVEN release.
%present it is downloaded from the corresponding raven-data release
%(https://github.com/SysBioChalmers/raven-data).
if ~isempty(dataDir)
hmmOptions={'kegg118_eukaryotes','kegg118_prokaryotes'};
if ~endsWith(dataDir,hmmOptions) %Check if dataDir ends with any of the hmmOptions.
Expand All @@ -224,7 +225,7 @@
else
fprintf('Downloading the HMM library file... ');
try
websave([libraryFile '.gz'],['https://github.com/SysBioChalmers/raven-toolbox/releases/download/v0.3.0/' hmmName '.hmm.gz']);
websave([libraryFile '.gz'],['https://github.com/SysBioChalmers/raven-data/releases/download/kegg118/' hmmName '.hmm.gz']);
catch ME
if strcmp(ME.identifier,'MATLAB:webservices:HTTP404StatusCodeError')
error('Failed to download the HMM library file, the server returned a 404 error, try again later. If the problem persists please report it on the RAVEN GitHub Issues page: https://github.com/SysBioChalmers/RAVEN/issues')
Expand Down
Loading