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Refine beta diversity utilities and remove scikit-bio dependency
…error handling for GO file downloads
…d alias for backward compatibility
Add HTML report CLI workflow
Enhance Peptide Direct to OTF workflow functionality by using MetaUmbra
- Bundled echarts.min.js and echarts-gl.min.js into the project (�ssets/pyecharts). - Added a new UI setting Use Local JS Assets to toggle offline mode. - Dynamically update Pyecharts ONLINE_HOST to switch between local file URI and remote CDN. - Resolved the slow initialization issue caused by CDN network latency.
… output collisions
Support unit specific OTF annotation and analysis
Enhance MGnify downloads and update dbCAN URL handling solve #16
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| resolved_peptide_col, resolved_protein_col = _resolve_digest_columns_once( | ||
| first_file=all_files[0], |
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In unit-specific folder mode, this resolves peptide/protein column names from only all_files[0] and then applies those names to every selected genome TSV. If the first selected file is malformed or has a different header, _resolve_digest_columns_once can fall back to the wrong positional columns, causing subsequent valid genome files to be skipped with usecols errors and leaving the global peptide-protein map empty. This affects runs where a bad genome TSV appears before otherwise valid Protein/Peptide files; resolve per file or choose the first file whose header can be inferred.
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Title: MetaX 2 end-to-end metaproteomics workflow
Description:
This PR merges the current
devbranch intomainand consolidates the major MetaX 2 updates.MetaX 2 is now positioned as an end-to-end, peptide-centric metaproteomics analysis platform. The updated workflow connects peptide evidence, MetaUmbra-based genome scope estimation, OTF construction, automated reporting, reproducible workflow export, and downstream statistical analysis.
Major updates
1. Peptide Direct to OTF
Added and improved the Peptide Direct to OTF workflow, allowing users to generate OTF tables directly from peptide-level search results from MAG-based workflows such as DIA-NN, MetaLab-MAG, and MetaLab-DIA.
2. MetaUmbra genome scope estimation
Integrated MetaUmbra into MetaX for genome scope estimation before OTF construction. MetaX can now run MetaUmbra scoring, reuse selected genome lists, or stop after genome-presence scoring.
3. Unit-specific OTF annotation
Added unit-specific OTF annotation, allowing different sample groups or analysis units to use distinct genome sets during peptide-to-OTF mapping. This supports MetaUmbra
unit_specific_manifest.jsonfiles and addsanalysis_unit_idto the output.4. Auto OTF Report
Added the Auto OTF Report module for one-click report generation from OTF analysis results. Reports include summary statistics, tables, plots, group-vs-control results, reproducibility metadata, and optional PNG/SVG/PDF figure outputs.
5. Limma-based differential analysis
Added limma support for differential expression analysis and made it the default DE method. The DE backend now uses InMoose, with improved input preparation, group-vs-control testing, stratified comparisons, and result extraction.
6. Workflow export to notebook
Added workflow recording and export support for GUI-based analyses. Users can export recorded workflows as a Jupyter notebook, Python script, and YAML file for reproducibility and downstream customization.
7. Database builder and updater improvements
Improved MGnify and dbCAN database handling, including new MGnify update sources, corrected download paths, more reliable dbCAN identifier merging, and safer cancellation/shutdown behavior during database downloads and annotation builds.
8. GUI and usability improvements
Updated the GUI to support MetaX 2 workflows, including new dialogs for Auto Report and unit-specific settings, improved Peptide Annotator controls, local ECharts assets, selected-item PCA plotting, and enhanced table export.
9. CLI and packaging updates
Added command-line entry points for
metax,metax-annotate, andmetax-report, and updated package dependencies to support MetaUmbra integration and the new reporting workflow.10. Documentation and tests
Updated the MetaX Cookbook, changelog, and documentation for the new MetaX 2 workflows. Added and updated tests for auto report generation, unit-specific OTF annotation, peptide table preparation, database updating, workflow export, plotting, and statistical analysis.
Overall impact
This merge upgrades MetaX into a more complete one-stop platform for peptide-centric metaproteomics analysis:
Peptides → genome scope estimation → OTF construction → reports → workflow export → downstream analysis