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TRON-Bioinformatics / covigator

CoVigator - Monitoring SARS-CoV-2 mutations
MIT License
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62 annotate lineages with described mutations #105

Closed johausmann closed 1 year ago

johausmann commented 1 year ago

With this merge request, we include the mutations in the DB that are described to define a given lineage. This addresses #62. Since the constellation mutation representation allows descriptions at the nucleotide and amino acid level, we translate SNVs and deletions to the protein level to obtain an HGVS representation in the database

codecov[bot] commented 1 year ago

Codecov Report

Patch coverage: 99.60% and project coverage change: +1.60 :tada:

Comparison is base (c642f8c) 83.91% compared to head (5910e67) 85.51%.

Additional details and impacted files ```diff @@ Coverage Diff @@ ## develop #105 +/- ## =========================================== + Coverage 83.91% 85.51% +1.60% =========================================== Files 47 48 +1 Lines 4421 4924 +503 =========================================== + Hits 3710 4211 +501 - Misses 711 713 +2 ``` | [Impacted Files](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/105?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics) | Coverage Δ | | |---|---|---| | [covigator/references/lineage\_annotation.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/105?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL3JlZmVyZW5jZXMvbGluZWFnZV9hbm5vdGF0aW9uLnB5) | `99.46% <99.31%> (-0.54%)` | :arrow_down: | | [covigator/\_\_init\_\_.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/105?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL19faW5pdF9fLnB5) | `100.00% <100.00%> (ø)` | | | [covigator/database/model.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/105?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL2RhdGFiYXNlL21vZGVsLnB5) | `98.82% <100.00%> (+0.03%)` | :arrow_up: | | [...r/tests/unit\_tests/test\_database\_initialisation.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/105?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL3Rlc3RzL3VuaXRfdGVzdHMvdGVzdF9kYXRhYmFzZV9pbml0aWFsaXNhdGlvbi5weQ==) | `100.00% <100.00%> (ø)` | | | [...igator/tests/unit\_tests/test\_lineage\_annotation.py](https://app.codecov.io/gh/TRON-Bioinformatics/covigator/pull/105?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=TRON-Bioinformatics#diff-Y292aWdhdG9yL3Rlc3RzL3VuaXRfdGVzdHMvdGVzdF9saW5lYWdlX2Fubm90YXRpb24ucHk=) | `100.00% <100.00%> (ø)` | |

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johausmann commented 1 year ago

Okay, let's move on to hopefully the last round of review :smile:

johausmann commented 1 year ago

All comments have been addressed. Merge coming soon :rocket: