AlphaPept Protein Group Reader - #327

Merged

lucas-diedrich merged 86 commits into

pg-reader-3-diannfrom

pg-reader-4-alphapept

Aug 26, 2025

Commits on Aug 21, 2025

[Feature] Add alphapept protein group matrix reader
lucas-diedrich
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700b156
[Doc] Add explanatory comments for magic values
lucas-diedrich
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0d1e91e
[Feature] Add configuration of alphapept protein group reader
lucas-diedrich
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cfc69d3
[Feature] Add keys for alphapept reader
lucas-diedrich
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79087aa
[Fix] Bug fix. Keep dataframe index if no features are specified and the length of feature_columns is 0
lucas-diedrich
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754453e
[Doc] Add explanatory comment
lucas-diedrich
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38d4c7d
[Fix] Fix type hint
lucas-diedrich
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7e2a310
[Tests] Unittests for the index parsing function of the alphapept reader
lucas-diedrich
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7ab7adf
[Fix] Bug fixes for the parsing of alphapept indices
lucas-diedrich
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6f71280
[Doc] Fix examples
lucas-diedrich
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abaacd7
[API] Expose alphapept reader
lucas-diedrich
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3ae462e
[Tests] Add integration tests for alphapet
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034047c
[Doc] Add examples
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80de4c9
[Tests] Use public AlphaPeptPGReader instead of module level import
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6d9cc76
[Typing] Add type hints to tests
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5b70307
[Doc] Fix incorrect reader name
lucas-diedrich
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65445cb
[Doc] Fix typo
lucas-diedrich
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4d8cc57
[Doc] Update docstring
lucas-diedrich
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bb300b1
[Fix] Incorporate suggestions from Copilot review
lucas-diedrich
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19d0ca4
[Doc] Fix typos in docstrings
lucas-diedrich
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6c59695
[Refactor] Refactor so that the method does not depend on custom load_files logic and also supports alphapept hdf reports
lucas-diedrich
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be74704
[Test] Add tests for alphapept hdf files
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0c01e84
[Feature] Implement pre-configured regular expressions
lucas-diedrich
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000b094
[Refactor] Restructure pg_reader_yaml to accomodate pre-configured regular expressions
lucas-diedrich
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b67b3f6
[Doc] Expose pre-configured keys in class init as type hints. Improve examples.
lucas-diedrich
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5c895b4
[Test] Add tests for _get_measurement_regex
lucas-diedrich
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5031247
[Test] Adjust test based on new config structure
lucas-diedrich
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a738164
[Tests] Remove unnecessary tests of reader_provider import
lucas-diedrich
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a6533c1
[Doc] Fix docstring
lucas-diedrich
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9be20bb
[Requirements] Add pytables dependency which is necessary to read hdf files
lucas-diedrich
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39ab064
[Tests] Add exact comparison for integration test
lucas-diedrich
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f083adb
[Doc] Clean up comments in config file
lucas-diedrich
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ec85043
[Config] Add column mapping explicitly to make explicity which index levels are found in the output dataframe
lucas-diedrich
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182a74d
[Doc] Cleaned up docstring
lucas-diedrich
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d4d16ea
[Fix] Fix missing import
lucas-diedrich
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48c227a
[Fix] Refactor conftests - skip gracefully if connection times out, add helper function that removes repetitive code
lucas-diedrich
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6162c0a

Commits on Aug 22, 2025

[Test] Make conftests only depend on local data if possible.
lucas-diedrich
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60a835e
[Test] Adjust expected shapes for alphapeptreader based on new testd data
lucas-diedrich
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f63a0e3
[Tests] Add test data
lucas-diedrich
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0422980
[Refactor] Move all constants to class constants
lucas-diedrich
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6fe8305
[Nit] Warn if unexpected format is encountered
lucas-diedrich
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27c1e37
[Fix] Remove unnecessary helper function
lucas-diedrich
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798ac79
[Feature] Configuration for MaxQuant reader
lucas-diedrich
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3891bcd
[Feature] Add post-processing method that acts on streamlined columns before they become the dataframe index
lucas-diedrich
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255c978
[API] Expose MaxQuantPGReader to users
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7c1de7d
[Feature] MaxQuant reader with documentation
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843108a
[Test] Add integration test for MaxQuantPGReader
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551f963

Commits on Aug 23, 2025

[Test] Adjust tests to work with local test data - MQReader
lucas-diedrich
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fe922c5
[Tests] Add test data
lucas-diedrich
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3b79dce
[Fix] Fix typo
lucas-diedrich
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9f4d3e7
[Doc] Update docstring, add more explicit parameter explanations
lucas-diedrich
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521fa13
[Doc] Update docstrings and remove incorrect copy documentation
lucas-diedrich
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3fd9d98
[Doc] Clarify docstring
lucas-diedrich
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7717cd2
[Feature] Spectronaut reader
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31e46e3
[Feature] Spectronaut reader config
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5aaf207
[API] Expose spectronaut reader to users
lucas-diedrich
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3cfc4ca
[Test] Spectronaut integration tests
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f28d73e
[Doc] Add examples
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4573149
[Fix] Rename pre-configured regex to default
lucas-diedrich
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c287cd2
[Fix] Fix typos
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4940a73
[Feature] Add parquet support. Specifically desirable for spectronaut reports which are also exported in parquet format
lucas-diedrich
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b5c7a9b
[Test] Add integration test for spectronaut.parquet report
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41eef70
[Doc] Add regular expression documentation
lucas-diedrich
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207e386
[Doc] Improve docstring of class initialization
lucas-diedrich
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ef71f1a
[Feature] Add additional column mapping for parquet report protein groups
lucas-diedrich
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a2427d7
[Test] Refactor tests so that they work with local data
lucas-diedrich
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0e13e68
[Test-Data] Add test data reference for spectronaut reports
lucas-diedrich
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5e9c1c0
[Feature] Implement fragpipe reader
lucas-diedrich
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85e05cb
[API] Expose FragPipeReader to users
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4a46205
[Tests] Add integration test for FragPipeReader
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808547b
[Fix] Fix typo in URL
lucas-diedrich
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38b995d
[Test] Update tests to work with local data (FragPipe PG reader)
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deccde6
[Test-data] Add test reference data (PG fragpipe)
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6cbe7d9
[Feature] Add MZTab protein group reader
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cc9b861
[API] Expose MZTab to users
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6699fac
[Tests] Add integration tests
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8e0e8c5
[Refactor] Set correct default values
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2a2848e
[Tests] Add integration tests
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00c72f0
[Test] Refactor mztab integration test so that it runs with local data
lucas-diedrich
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86eeb7a
[Test-data] Add local test data (mzTAB PG Reader)
lucas-diedrich
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15545aa
[Doc] Add PG-reader API docs
lucas-diedrich
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0343aeb

Commits on Aug 26, 2025