Spectronaut PG Reader - #331
Merged
Merged
Conversation
lucas-diedrich
requested review from
Copilot and
mschwoer
and removed request for
mschwoer
August 11, 2025 18:45
There was a problem hiding this comment.
Pull Request Overview
This PR implements a Spectronaut protein group reader for processing pivot reports from the Spectronaut search engine. The implementation includes custom post-processing to handle "Filtered" values in the report by replacing them with NaN values.
Key changes:
- Added SpectronautPGReader class with custom post-processing for "Filtered" values
- Integrated the reader into the provider system and main module exports
- Added comprehensive test coverage and configuration for Spectronaut data format
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/spectronaut_reader.py | Main implementation of SpectronautPGReader with post-processing logic |
| alphabase/pg_reader/init.py | Export SpectronautPGReader in module public API |
| alphabase/constants/const_files/pg_reader.yaml | Configuration mapping for Spectronaut column names and regex patterns |
| tests/integration/test_pg_readers.py | Integration tests for the new reader functionality |
| tests/integration/test_pg_reader_provider.py | Tests for provider registration |
| tests/integration/conftest.py | Test fixture for downloading example Spectronaut data |
Collaborator
Author
|
Added parquet support. |
mschwoer
approved these changes
Aug 13, 2025
mschwoer
left a comment
mschwoer
left a comment
Contributor
There was a problem hiding this comment.
LGTM, but have a look at my previoud comments regarding
- examples in docstrings
- regexp docu
- test data downloading
lucas-diedrich
force-pushed
the
pg-reader-5-maxquant
branch
2 times, most recently
from
August 23, 2025 09:55
90884b3 to
3b79dce
Compare
… reports which are also exported in parquet format
lucas-diedrich
force-pushed
the
pg-reader-6-spectronaut
branch
from
August 23, 2025 10:32
173d893 to
5e9c1c0
Compare
API documentation for PG reader
MZTab protein group reader
FragPipe PG Reader
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Spectronaut protein group reader.
Implement spectronaut protein group reader based on
pivot report(Spectronaut Manual, Page 80)With custom post-processing method to get rid of "Filtered" values in report table.