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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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bug fix Modification Info List which reports the the modification stoichiometry in PSM counts and fractions on the full protein sequence #2321

Closed trishorts closed 9 months ago

trishorts commented 10 months ago

The protein groups output has a column that is labeled "Modification Info List" that reports the count of psms for each localized PTM relative to the count of all PSMs containing that amino acid position. See example below. The currently reported number is incorrect. I believe this error comes from a failure to apply the ".Resolve" method that we use for writing the AllPSMs.psmtsv. This PR provides the correct number.

aa279[N->D on N,info:occupancy=0.04(1/28)];#aa285[N->D on N,info:occupancy=0.40(12/30)];#aa390[N->D on N,info:occupancy=0.17(1/6)];#aa398[N->D on N,info:occupancy=1.00(5/5)]

codecov[bot] commented 10 months ago

Codecov Report

Merging #2321 (32f96ad) into master (a7c4c7f) will decrease coverage by 0.01%. The diff coverage is 100.00%.

Additional details and impacted files [![Impacted file tree graph](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2321/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/2321?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 #2321 +/- ## ========================================== - Coverage 92.67% 92.67% -0.01% ========================================== Files 135 135 Lines 20995 20994 -1 Branches 2880 2880 ========================================== - Hits 19457 19456 -1 Misses 1063 1063 Partials 475 475 ``` | [Files](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc) | Coverage Δ | | |---|---|---| | [...pheus/EngineLayer/ProteinParsimony/ProteinGroup.cs](https://app.codecov.io/gh/smith-chem-wisc/MetaMorpheus/pull/2321?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=smith-chem-wisc#diff-TWV0YU1vcnBoZXVzL0VuZ2luZUxheWVyL1Byb3RlaW5QYXJzaW1vbnkvUHJvdGVpbkdyb3VwLmNz) | `95.04% <100.00%> (-0.01%)` | :arrow_down: |