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smith-chem-wisc / MetaMorpheus

Proteomics search software with integrated calibration, PTM discovery, bottom-up, top-down and LFQ capabilities
MIT License
90 stars 45 forks source link

Pep bug fix #2374

Closed Alexander-Sol closed 2 weeks ago

Alexander-Sol commented 3 weeks ago

Fixed an issue where PEP was duplicating PSMs when creating training data.

Fixed SpectralRecoveryTests (Those tests depended on duplicating one decoy PSM 4 times in order for PEP to run. Once PSMs were no longer duplicated, PEP broke. Fixed the test by adding in three additional decoys)

Also, edited the PostSearchAnalysisTaskTest. We now see fewer PSMs with PEP-Q < 0.01 and more peptides with PEP-Q < 0.01. The test has been edited to reflect that.

codecov[bot] commented 3 weeks ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Project coverage is 92.86%. Comparing base (661b1e5) to head (bf83d24). Report is 2 commits behind head on master.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2374/graphs/tree.svg?width=650&height=150&src=pr&token=m0HXyK8tFy&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2374?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) ```diff @@ Coverage Diff @@ ## master #2374 +/- ## ========================================== + Coverage 92.81% 92.86% +0.04% ========================================== Files 137 137 Lines 21170 21199 +29 Branches 2924 2929 +5 ========================================== + Hits 19649 19686 +37 + Misses 1042 1038 -4 + Partials 479 475 -4 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2374?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2374?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FFdrAnalysis%2FPEPValueAnalysisGeneric.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0ZkckFuYWx5c2lzL1BFUFZhbHVlQW5hbHlzaXNHZW5lcmljLmNz) | `96.15% <100.00%> (+0.05%)` | :arrow_up: | | [...us/TaskLayer/MbrAnalysis/SpectralRecoveryRunner.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2374?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FMbrAnalysis%2FSpectralRecoveryRunner.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9NYnJBbmFseXNpcy9TcGVjdHJhbFJlY292ZXJ5UnVubmVyLmNz) | `91.46% <ø> (ø)` | | ... and [9 files with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2374/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc)