Feature: add exporting "score_peptide" and "score_protein" from .osw#159
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singjc merged 4 commits intoPyProphet:masterfrom Aug 22, 2025
Merged
Feature: add exporting "score_peptide" and "score_protein" from .osw#159singjc merged 4 commits intoPyProphet:masterfrom
singjc merged 4 commits intoPyProphet:masterfrom
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Thanks for adding! I just made a minor suggestion which you can commit, for snakecase syntax. Just double check in case I missed one, we can the merge afterwards.
pyprophet/io/export/osw.py
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| # Non-global contexts pivot query | ||
| if pivot_cols_str: # Only if there are non-global contexts | ||
| nonGlobal_query = f""" |
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| nonGlobal_query = f""" | |
| non_global_query = f""" |
Convert to snakecase for consistency.
pyprophet/io/export/osw.py
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| """ | ||
| else: | ||
| # If no non-global contexts, create empty result with same structure | ||
| nonGlobal_query = f""" |
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| nonGlobal_query = f""" | |
| non_global_query = f""" |
pyprophet/io/export/osw.py
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| g.{score_table}_GLOBAL_PVALUE, | ||
| g.{score_table}_GLOBAL_QVALUE, | ||
| g.{score_table}_GLOBAL_PEP | ||
| FROM ({nonGlobal_query}) ng |
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| FROM ({nonGlobal_query}) ng | |
| FROM ({non_global_query}) ng |
pyprophet/io/export/osw.py
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| """ | ||
| elif pivot_cols_str and not global_exists: | ||
| # Only non-global contexts exist | ||
| merged_query = nonGlobal_query |
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| merged_query = nonGlobal_query | |
| merged_query = non_global_query |
change to snakecase syntax
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Thanks for the quick review, addressed the comments (you did not miss any cases) so I think it is ready to merge. |
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Currently exporting .osw to .oswpq does not include protein and peptide scores/pep/qvalues. This functionality is important when have a pre-analyzed .osw files that we want to convert to .oswpq for easier data access (e.g. in massdash)
This was tested with the test.osw file in massdash (file path
/test/test_data/example_dia/openswath/osw) and seems to yield expected results.