topdownproteomics / sdk

Software solution for common top-down proteomics tasks
http://www.topdownproteomics.org/
MIT License
9 stars 4 forks source link

Fix to RESID ProForma writing #108

Closed mtrobey closed 1 year ago

mtrobey commented 1 year ago

In most test cases, we show ProFormaDescriptor with a mod identifier usage as:

new ProFormaDescriptor(ProFormaKey.Identifier, ProFormaEvidenceType.PsiMod, "MOD:00232")

where the full accepted CV term is used as the "value."

For RESID, we instead had:

new ProFormaDescriptor(ProFormaKey.Identifier, ProFormaEvidenceType.Resid, "AA0420"), with the ProForma writer adding "RESID." This caused the writer to display "RESID:RESID:AA0420" in cases where the user used the full "RESID:AA0420" accession.

Updates so that different mod ontologies are handled consistently.

Also updates README to reflect change to the ProFormaDescriptor constructor signature.

codecov[bot] commented 1 year ago

Codecov Report

Merging #108 (8993db6) into master (1412892) will not change coverage. The diff coverage is 100.00%.

:exclamation: Current head 8993db6 differs from pull request most recent head 6fac795. Consider uploading reports for the commit 6fac795 to get more accurate results

Additional details and impacted files [![Impacted file tree graph](https://codecov.io/gh/topdownproteomics/sdk/pull/108/graphs/tree.svg?width=650&height=150&src=pr&token=T8Kf00TGxl&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=topdownproteomics)](https://codecov.io/gh/topdownproteomics/sdk/pull/108?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=topdownproteomics) ```diff @@ Coverage Diff @@ ## master #108 +/- ## ======================================= Coverage 84.68% 84.68% ======================================= Files 102 102 Lines 5545 5545 ======================================= Hits 4696 4696 Misses 849 849 ``` | [Impacted Files](https://codecov.io/gh/topdownproteomics/sdk/pull/108?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=topdownproteomics) | Coverage Δ | | |---|---|---| | [src/TopDownProteomics/ProForma/ProFormaWriter.cs](https://codecov.io/gh/topdownproteomics/sdk/pull/108?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=topdownproteomics#diff-c3JjL1RvcERvd25Qcm90ZW9taWNzL1Byb0Zvcm1hL1Byb0Zvcm1hV3JpdGVyLmNz) | `94.20% <100.00%> (ø)` | |