MaxQuant ProteinGroup Reader - #330
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Pull Request Overview
This PR introduces a protein group (PG) reader framework for MaxQuant and other proteomics search engines. The implementation provides a standardized interface for reading protein group tables from different search engines with support for multiple intensity types.
Key changes:
- Implements
PGReaderBaseclass with standardized protein group reading functionality - Adds specific readers for MaxQuant, AlphaPept, DIANN, and AlphaDIA search engines
- Supports 3 different intensity types (raw, LFQ, iBAQ) with configurable regex patterns
Reviewed Changes
Copilot reviewed 18 out of 19 changed files in this pull request and generated 3 comments.
Show a summary per file
| File | Description |
|---|---|
| alphabase/pg_reader/pg_reader.py | Core base class and provider for all protein group readers |
| alphabase/pg_reader/maxquant_pg_reader.py | MaxQuant-specific reader with decoy indicator post-processing |
| alphabase/pg_reader/alphapept_pg_reader.py | AlphaPept reader with complex protein identifier parsing |
| alphabase/pg_reader/keys.py | Standardized column constants for protein group data |
| alphabase/constants/const_files/pg_reader.yaml | Configuration mappings for different search engines |
| requirements/requirements.txt | Added tables dependency for HDF file support |
| tests/ | Comprehensive unit and integration test suite |
mschwoer
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… before they become the dataframe index
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… reports which are also exported in parquet format
API documentation for PG reader
MZTab protein group reader
FragPipe PG Reader
Spectronaut PG Reader
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Protein group reader for MaxQuant protein group tables
Implementation
New features
Needs to implement
_post_processmethod, analogous to_pre_processmethod to efficiently standardizeis_decoycolumn