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corneliusroemer
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Really good
The level definitions are somewhat arbitrary at the boundaries - they are informed by what we commonly see - could be subject to change.
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Excellent stuff @jameshadfield.
It's great, definitely already useful as is, could just merge and improve over time. Maybe greying out non-21L descendants is the only important change. |
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Thanks @corneliusroemer. I'll move the definitions out of a script into a config (easy), change the name to |
For background please see "Variant report 2022-10-17" section of https://github.com/neherlab/SARS-CoV-2_variant-reports/blob/main/reports/variant_report_latest_draft.md for details of lineage classification. Additional changes via @corneliusroemer in #1018. Note that the mutations are relative to BA.2 so we should really use this for omicron-only builds, which are being developed elsewhere. This is especially relevant for S:493 where we consider a reversion to increase the level, meaning strains basal to BA.2 will be elevated inappropriately.
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Applied @corneliusroemer's changes to the definitions and generally made this PR into something that is maintainable going forward. Changes to the level definitions are made by modifying But I see that CI has failed because "ERROR: no node found with a clade_annotation of 21L (Omicron)". We want to allow this to work on all trees, even if they don't have any omicron sequences, so I'll update this now. |
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Test builds (GenBank this time) running now. I'll merge this as long as it completes succsessfully: --> Trial name is: feat-levels-mk2 --> When completed, the following will be available: --> You can attach to this AWS job via: --> View this job in the AWS console via |
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That trial build failed, here's another one... --> Trial name is: feat-levels-mk3 --> When completed, the following will be available: --> You can attach to this AWS job via: --> View this job in the AWS console via |
For background please see "Variant report 2022-10-17" section of https://github.com/neherlab/SARS-CoV-2_variant-reports/blob/main/reports/variant_report_latest_draft.md for details of lineage classification. Additional changes via @corneliusroemer in #1018. Note that the mutations are relative to BA.2 so we should really use this for omicron-only builds, which are being developed elsewhere. This is especially relevant for S:493 where we consider a reversion to increase the level, meaning strains basal to BA.2 will be elevated inappropriately.
They are only defined in this context, so it's not a good idea to apply these rules to other sequences!
this can happen when running (e.g) trees without omicron sequences as part of the ncov pipeline and we don't want this to be a fatal error. In these situations the script will export a node-data JSON with no node-data, and thus the coloring won't be available to auspice.
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[the following discussion from slack]
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For background please see "Variant report 2022-10-17" section of https://github.com/neherlab/SARS-CoV-2_variant-reports/blob/main/reports/variant_report_latest_draft.md for details of lineage classification. This commit is very much a first pass to see if (a) it works robustly on large datasets and (b) there is interest in including it (there is from me!)
Note that the mutations are relative to BA.2 so we should really use this for omicron-only builds, which are being developed elsewhere. This is especially relevant for S:493 where we consider a reversion to increase the level, meaning strains basal to BA.2 will be elevated inappropriately.
Trial builds via https://github.com/nextstrain/ncov/actions/runs/3278003787.
nextstrain URLs: https://nextstrain.org/staging/ncov/gisaid/trial/feat-levels/REGION_NAME
e.g. https://nextstrain.org/staging/ncov/gisaid/trial/feat-levels/global/2m
You can attach to this AWS job via:
nextstrain build --aws-batch --attach 08b4c304-03ea-49f6-af22-f60102f14896 /home/runner/work/ncov/ncovView this job in the AWS console via
https://console.aws.amazon.com/batch/home?region=us-east-1#jobs/detail/08b4c304-03ea-49f6-af22-f60102f14896
cc @corneliusroemer