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compomics / psm_utils

Common utilities for parsing and handling peptide-spectrum matches and search engine results in Python
https://psm-utils.readthedocs.io
Apache License 2.0
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Updated msamanda.py to include new column names in the MS Amanda output CSV file #37

Closed louisebuur closed 1 year ago

louisebuur commented 1 year ago

Output files from the newest version of MS Amanda (3.0) includes additional columns with additional features, so this update insures that these additional columns are also read in. I implemented this simply by adding the new column names to the "REQUIRED_COLUMNS" list To test the changes I also updated test_msamanda.py to include the new column names I also added the documentation for the MS Amanda module

Changelog:

FIxed

Changed

codecov-commenter commented 1 year ago

Codecov Report

Patch coverage: 83.33% and project coverage change: +0.43 :tada:

Comparison is base (b1d6c94) 42.04% compared to head (c134cf2) 42.47%.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## main #37 +/- ## ========================================== + Coverage 42.04% 42.47% +0.43% ========================================== Files 19 19 Lines 1527 1535 +8 ========================================== + Hits 642 652 +10 + Misses 885 883 -2 ``` | [Impacted Files](https://app.codecov.io/gh/compomics/psm_utils/pull/37?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics) | Coverage Δ | | |---|---|---| | [psm\_utils/io/msamanda.py](https://app.codecov.io/gh/compomics/psm_utils/pull/37?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=compomics#diff-cHNtX3V0aWxzL2lvL21zYW1hbmRhLnB5) | `77.41% <83.33%> (+7.04%)` | :arrow_up: |

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RalfG commented 1 year ago

Thanks for the PR! I updated the code to directly add potential rescoring features to the rescoring_features field. The new example also contains the columns Weighted Probability and Nr of matched peaks. Can these also be added to the list of potential rescoring features?

louisebuur commented 1 year ago

The new example also contains the columns Weighted Probability and Nr of matched peaks. Can these also be added to the list of potential rescoring features?

Yes! Definitely! Sorry I overlooked that!