FragPipe PG Reader - #332
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Pull Request Overview
This PR adds a new reader for FragPipe protein group output files (protein.tsv) to support parsing FragPipe proteomics analysis results.
- Introduces
FragPipePGReaderclass with support for multiple intensity measurement types (raw, razor, unique, total, LFQ variants) - Adds configuration mapping for FragPipe-specific column names and measurement regex patterns
- Includes comprehensive test coverage with integration tests and reader provider tests
Reviewed Changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated 2 comments.
Show a summary per file
| File | Description |
|---|---|
| alphabase/pg_reader/fragpipe_pg_reader.py | New FragPipe reader implementation with support for multiple measurement types |
| alphabase/pg_reader/init.py | Export new FragPipePGReader class |
| alphabase/constants/const_files/pg_reader.yaml | Configuration for FragPipe column mappings and measurement regex patterns |
| tests/integration/test_pg_readers.py | Integration tests for FragPipe reader functionality |
| tests/integration/test_pg_reader_provider.py | Tests for reader provider registration |
| tests/integration/conftest.py | Test fixture for FragPipe example data |
mschwoer
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Aug 13, 2025
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nice! the small amount of code needed is a indicator that the base class is well-designed
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API documentation for PG reader
MZTab protein group reader
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Reader for FragPipe output
Documented here: https://fragpipe.nesvilab.org/docs/tutorial_fragpipe_outputs.html#proteintsv