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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
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Add the comment on glyco-searching and the search summary on the result file #2367

Open RayMSMS opened 1 month ago

RayMSMS commented 1 month ago

  1. Add lei's comment on the coding of o-pair searching.

  2. Try to add the search summary information (PSMs, protein group, glycoPsms, Level1-glycoPsms) into the "AllResult.txt" file for glycoSearch (1) Text function in PostGlycoSearchAnalysisTask class (2) Tester in TestOGlyco class (make sure we parse the certain value) (3) revise the "readCsv", and enable it to read the allPSMs file smoothly.

codecov[bot] commented 1 month ago

Codecov Report

Attention: Patch coverage is 89.70588% with 28 lines in your changes missing coverage. Please review.

Project coverage is 93.46%. Comparing base (9b3118c) to head (359154d). 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/2367/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/2367?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 #2367 +/- ## ========================================== + Coverage 92.89% 93.46% +0.56% ========================================== Files 139 139 Lines 21435 21497 +62 Branches 2944 2966 +22 ========================================== + Hits 19913 20092 +179 + Misses 1043 939 -104 + Partials 479 466 -13 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?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 | | |---|---|---| | [MetaMorpheus/EngineLayer/GlycoSearch/AdjNode.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FAdjNode.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0Fkak5vZGUuY3M=) | `80.00% <ø> (ø)` | | | [MetaMorpheus/EngineLayer/GlycoSearch/GlycanBox.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FGlycanBox.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0dseWNhbkJveC5jcw==) | `81.81% <100.00%> (ø)` | | | [...pheus/EngineLayer/GlycoSearch/LocalizationGraph.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FLocalizationGraph.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0xvY2FsaXphdGlvbkdyYXBoLmNz) | `100.00% <100.00%> (ø)` | | | [MetaMorpheus/EngineLayer/GlycoSearch/ModBox.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FModBox.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL01vZEJveC5jcw==) | `90.90% <ø> (ø)` | | | [MetaMorpheus/EngineLayer/GlycoSearch/Node.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FNode.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL05vZGUuY3M=) | `88.00% <ø> (+21.33%)` | :arrow_up: | | [MetaMorpheus/EngineLayer/PsmTsv/PsmFromTsv.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FPsmTsv%2FPsmFromTsv.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1BzbVRzdi9Qc21Gcm9tVHN2LmNz) | `97.74% <100.00%> (+0.04%)` | :arrow_up: | | [...pheus/TaskLayer/GlycoSearchTask/GlycoSearchTask.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree&filepath=MetaMorpheus%2FTaskLayer%2FGlycoSearchTask%2FGlycoSearchTask.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL1Rhc2tMYXllci9HbHljb1NlYXJjaFRhc2svR2x5Y29TZWFyY2hUYXNrLmNz) | `97.59% <100.00%> (ø)` | | | [MetaMorpheus/EngineLayer/GlycoSearch/Glycan.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FGlycan.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0dseWNhbi5jcw==) | `97.00% <96.66%> (+0.21%)` | :arrow_up: | | [...aMorpheus/EngineLayer/GlycoSearch/GlycoPeptides.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FGlycoSearch%2FGlycoPeptides.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL0dseWNvU2VhcmNoL0dseWNvUGVwdGlkZXMuY3M=) | `88.03% <94.11%> (ø)` | | | [...eus/EngineLayer/ModernSearch/ModernSearchEngine.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree&filepath=MetaMorpheus%2FEngineLayer%2FModernSearch%2FModernSearchEngine.cs&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL01vZGVyblNlYXJjaC9Nb2Rlcm5TZWFyY2hFbmdpbmUuY3M=) | `74.54% <85.71%> (ø)` | | | ... and [4 more](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | | ... and [3 files with indirect coverage changes](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2367/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)