Recent Releases of predectorutils
predectorutils - 1.2.7
What's Changed
- Copy result files to results folder instead of linking by @IdoBar in https://github.com/ccdmb/predector/pull/85
- Updates deepredeff implementation to use plain python. Avoids issue using R and reticulate inside conda environment.
- New version of predector utils adds tool to map protein results onto genome coordinates for visualisation.
Full Changelog: https://github.com/ccdmb/predector/compare/1.2.6...1.2.7
- Shell
Published by darcyabjones over 3 years ago
predectorutils - 1.2.7-alpha
What's Changed
- Copy result files to results folder instead of linking by @IdoBar in https://github.com/ccdmb/predector/pull/85
Full Changelog: https://github.com/ccdmb/predector/compare/1.2.6...1.2.7-alpha
- Shell
Published by darcyabjones over 3 years ago
predectorutils - 1.2.6
What's Changed
- Remove pinning of python to v3.6 by @IdoBar in https://github.com/ccdmb/predector/pull/80
- New release by @darcyabjones in https://github.com/ccdmb/predector/pull/83
- Fixes bug causing protein names to be "." in individual results tables.
New Contributors
- @IdoBar made their first contribution in https://github.com/ccdmb/predector/pull/80
Full Changelog: https://github.com/ccdmb/predector/compare/1.2.5...1.2.6
- Shell
Published by darcyabjones almost 4 years ago
predectorutils - 1.2.6-alpha
What's Changed
- 1.2.5 tag by @darcyabjones in https://github.com/ccdmb/predector/pull/76
- Remove pinning of python to v3.6 by @IdoBar in https://github.com/ccdmb/predector/pull/80
- Pinned to python 3.9
- Updated dependencies.
- Fixed bug causing names to be absent from some results tables.
New Contributors
- @IdoBar made their first contribution in https://github.com/ccdmb/predector/pull/80
Full Changelog: https://github.com/ccdmb/predector/compare/1.2.5...1.2.6-alpha
- Shell
Published by darcyabjones almost 4 years ago
predectorutils - 1.2.5
What's Changed
- Update to work with SignalP 6.0g
- Fixes issue with installer calling chmod -R . failing
NOTE. SignalP 6.0g was distributed with the GPU model, this installer not backwards compatible.
Full Changelog: https://github.com/ccdmb/predector/compare/1.2.4...1.2.5
- Shell
Published by darcyabjones about 4 years ago
predectorutils - 1.2.4
Incorporates new version of SignalP 6, other bug-fixes, and new options for skipping analyses.
- SignalP 6.0e support now added, with the suggested patch in https://github.com/fteufel/signalp-6.0/issues/3. There are still known issues with 6.0e so I was waiting for the update, but it's probably worth having this now.
- Fixed a bug in decode_seqs that could cause error if only one file goes into it. (in which case it will be symlinked as just the extension, so the file looks like a dotfile and isn't captured by the glob.
- Added support to not install signalp6 in the environment. In this case the pipeline will automatically detect that it isn't installed and skip the analysis.
- Added flags to not do perform the analyses: signalp 6, pfamscan, dbcan searches, effectordb searches, phibase searches.
- Added flag to control the batch size for signalp6 to control memory usage.
Full Changelog: https://github.com/ccdmb/predector/compare/1.2.3...1.2.4
- Shell
Published by darcyabjones about 4 years ago
predectorutils - 1.2.3
Adds support for SignalP 6.0c.
This is functionally identical to 6.0b. I filed a bug report, and they fixed it really quickly. The results are the same, the installer is the same. 6.0c just handles a really niche case if you happen to have something that looks like a bacterial SP.
Full Changelog: https://github.com/ccdmb/predector/compare/1.2.2...1.2.3
- Shell
Published by darcyabjones over 4 years ago
predectorutils - 1.2.2
Adds support for SignalP 6.0b. Update broke previous installers, and they don't keep the old versions around.
- Shell
Published by darcyabjones over 4 years ago
predectorutils - 1.2.1
What's Changed
Adds new analyses: - deepredeff - Regular expression matches to Kex2 cutsites and RXLR-like motifs. - Updated sequence searches against a new database of effector HMMs https://doi.org/10.6084/m9.figshare.16973665
General improvements - Extended documentation - New columns added to ranking table. - Utility scripts now use SQLite to scale better without using too much RAM. - New feature to use previously computed results. - Bug fixes in TargetP results parsing.
New Contributors
- @fmobegi made their first contribution in https://github.com/ccdmb/predector/pull/60
Full Changelog: https://github.com/ccdmb/predector/compare/1.1.1...1.2.1
- Shell
Published by darcyabjones over 4 years ago
predectorutils - 1.2.1-alpha
Fix to get deepredeff working
Full Changelog: https://github.com/ccdmb/predector/compare/1.1.1...1.2.1-alpha
- Shell
Published by darcyabjones over 4 years ago
predectorutils - 1.2.0-beta
This version introduces:
- deepredeff predictions
- regular expression matches to Kex2 cutsite and RxLR-like motifs
- updated Pfam reporting
- updated list of virulence related Pfam and dbCAN profiles
- Searches against a HMM database of effectors (previously used a blast-like search).
- Signal peptide cutsites in main ranking table
- Inclusion of deepredeff and signalp6 in the manual ranking score.
- Updated documentation
- Improved utility scripts to reduce memory use
- A feature to use pre-computed results.
Full Changelog: https://github.com/ccdmb/predector/compare/1.1.1...1.2.0-beta
- Shell
Published by darcyabjones over 4 years ago
predectorutils - 1.1.1
Minor patch changing default download location of Pfam, which has changed recently
- Shell
Published by darcyabjones over 4 years ago