Add/im boundaries to tsv export#175
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singjc merged 8 commits intoPyProphet:masterfrom Nov 28, 2025
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…er and SplitParquetReader
…n definitions for clarity
- Introduced columns: EXP_IM, IM_leftWidth, and IM_rightWidth to the output file. - Updated the output format to accommodate the additional ion mobility information. - Ensured compatibility with existing data structures while expanding the dataset.
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This pull request improves the robustness and maintainability of the OSW file reading logic in
pyprophet/io/export/osw.pyby centralizing and standardizing how ion mobility (IM) columns are handled. The main changes ensure that the code gracefully supports both older and newer OSW files, regardless of whether specific IM columns are present, and reduces code duplication by introducing helper methods.Ion Mobility (IM) column handling improvements:
_has_im_boundariesand_has_imto centralize checks for the presence of IM-related columns (EXP_IM,EXP_IM_LEFTWIDTH,EXP_IM_RIGHTWIDTH) in theFEATUREtable, improving code clarity and maintainability._read_unscored_data,_read_peptidoform_data,_read_augmented_data,_read_standard_data) to dynamically include IM columns or NULLs based on their presence, using the new helper methods. This ensures compatibility with both legacy and current OSW files. [1] [2] [3] [4] [5] [6] [7]Code organization and imports:
osw.py, removing unused imports and grouping related functionality for better readability.