Fix #4909 - Tavtigian Bayesian point sums #4920
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Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #4920 +/- ##
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- Coverage 84.80% 84.78% -0.03%
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Files 320 320
Lines 19335 19370 +35
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+ Hits 16397 16422 +25
- Misses 2938 2948 +10 ☔ View full report in Codecov by Sentry. |
dnil
commented
Oct 8, 2024
| @@ -112,15 +114,6 @@ <h4>Evidence of {{ category }}</h4> | |||
| </div> | |||
| {% endblock %} | |||
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| {% macro preview() %} | |||
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Ok, beginning to like the style; let's see what you think! |
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Ok, added tests, and "end states" outside VUS for P/LP and B/LB. |
dnil
commented
Oct 10, 2024
| prediction(str): in ['uncertain_significance','benign','likely_benign', | ||
| 'likely_pathogenic','pathogenic'] | ||
| def get_acmg_criteria(acmg_terms: set) -> tuple: |
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Refactored slightly to have one function to sort the terms, that can be reused by both the Richards and the Tavtigian classifier.
* Fix #4906 - warn on potentially conflicting ACMG terms. * add a tuple, sort, and simplify slightly * add test * typo * Update scout/constants/acmg.py Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com> * Update scout/utils/acmg.py Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com> --------- Co-authored-by: Chiara Rasi <rasi.chiara@gmail.com>
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This PR adds a functionality: Bayesian point sums for an alternative ACMG classification, and temperature for VUS.
Ok! I will brush up the visuals and add some tests, but kinda looks promising! 🌶️
Testing on cg-vm1 server (Clinical Genomics Stockholm)
Prepare for testing
scout-stageand the server iscg-vm1.ssh <USER.NAME>@cg-vm1.scilifelab.sesudo -iu hiseq.clinicalssh localhostpodman pssystemctl --user stop scout.targetsystemctl --user start scout@<this_branch>systemctl --user status scout.targetscout-stage) to be used for testing by other users.Testing on hasta server (Clinical Genomics Stockholm)
Prepare for testing
ssh <USER.NAME>@hasta.scilifelab.seus; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.conda activate S_scout; pip freeze | grep scout-browserbash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>us; scout --versionpaxaprocedure, which will release the allocated resource (scout-stage) to be used for testing by other users.How to test:
Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.
Review: