How whitehead/plaac works
PLAAC analyzes protein FASTA sequences for prion-like subsequences and returns ranked per-protein scores and candidate regions. Users can run the Java CLI directly or through the Python wrapper; the web application accepts uploads, runs jobs, and offers candidate results and visualization downloads. Background amino-acid frequencies configure analyses, and a yeast spreadsheet utility enriches result tables. The web excerpts show job setup, result handling, and visualization, but omit route and command construction details, so those links are not asserted. The web server is documented as using the same Java application as the CLI.
Main entry points: server.rb Web application · plaac.java Java CLI · __init__.py Python wrapper · job.rb Job runner
Components 14
User interfaces
- Java CLI
cli/src/plaac.java - Python wrapper
cli/python/src/plaac/__init__.py - Web application
web/lib/server.rb
Sequence analysis
- HMM scoring
cli/src/plaac.java
Web jobs and results
- Job runner
web/lib/job.rb - Job workspace
web/lib/job.rb - Candidate results
web/lib/server.rb - Candidate visualization
web/lib/server.rb
Analysis data and exports
- Background frequencies
web/bg_freqs - Yeast spreadsheet export
web/bin/fancy-yeast-spreadsheet.py
Other components
- CLI user
- Python user
- Web user
- Spreadsheet user
Connections 14
- CLI user → Java CLI: runs analysis
README.md - Python user → Python wrapper: calls wrapper
cli/python/src/plaac/__init__.py - Python wrapper → Java CLI: launches Java
cli/python/src/plaac/__init__.py - Java CLI → HMM scoring: scores sequences
cli/src/plaac.java - Web user → Web application: submits sequences
README.md - Web application → Job runner: creates job
web/lib/server.rb - Job runner → Job workspace: writes job files
web/lib/job.rb - Web application → Job workspace: reads results
web/lib/server.rb - Web application → Candidate results: loads candidates
web/lib/server.rb - Web application → Candidate visualization: generates details
web/lib/server.rb - Web application → Background frequencies: reads frequencies
web/lib/server.rb - Web application → Java CLI: uses Java analysis
README.md - Spreadsheet user → Yeast spreadsheet export: exports results
web/bin/fancy-yeast-spreadsheet.py - Candidate results → Yeast spreadsheet export: enriches TSV
web/bin/fancy-yeast-spreadsheet.py