N-glyco search improvements #2322
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Additional details and impacted files@@ Coverage Diff @@
## master #2322 +/- ##
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- Coverage 92.68% 92.67% -0.02%
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Files 136 137 +1
Lines 21302 21262 -40
Branches 2924 2928 +4
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- Hits 19744 19704 -40
+ Misses 1086 1080 -6
- Partials 472 478 +6
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lonelu
approved these changes
Dec 28, 2023
nbollis
approved these changes
Jan 2, 2024
| "AllPSMs.psmtsv", | ||
| "_AllProteinGroups.tsv", |
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Alexander-Sol
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Jan 10, 2024
nbollis
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Feb 14, 2024
* Updated Mzlib and made it so there are no errors on build * Adjusted digestionparams toml * fixed indexing engine without having a default product type * Fixed silac test * All Tests Pass! * Added toml test for new digestionparams * ope. Switched to proper version of mzLib * Added Omics to project.wxs * Updated ParsimonySequence to use interfaces * N-glyco search improvements (#2322) * reverted filtering method for psms passed to FlashLFQ * refactor glycospsmwriter and split from xlwriter * fix unit tests * rename N and O glyco test classes * refactor is patially working * files written to correct directory * now with glyco protein parsimony and writing all quantified proteins * nglycoBugged * n glyco output is correct now i think * yo * fix unit tests * fix more unit tests * dont need glyco stuff in writexl anymore * n glyco individual file unit test --------- Co-authored-by: Alex <AlexSolivais@gmail.com> Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu> * updated mzlib version --------- Co-authored-by: trishorts <mshort@chem.wisc.edu> Co-authored-by: Alex <AlexSolivais@gmail.com> Co-authored-by: MICHAEL SHORTREED <mrshortreed@wisc.edu>
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Addition of glyco-quant had previously messed up the N-glycan search. This PR fixes those bugs and properly handles output from O-, N- and ON-glyco combined search allowing quant and creation of individual file results with reporting of the correct motifs.