2y build targets #14
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2y build targets #14
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…ut the clock rate and clock rate standard deviation for the 2 year build
…ild and an all-time build. This commit introduces this new wildcard structure, as well as new functions for assigning strict clock rates for the 3 year trees
…h5nx and h5n1 should get 3 year builds
This switches from the older Augur subsampling strategy of --sequences-per-group to the newer --subsampling-max-sequences. By doing this, we can just specific once the target sequence count and don't have to play around with logic for different subtypes / time-spans. This also makes it easier to rapidly test entire set of builds by locally swapping from "3000" to "100" in just one line.
I'd suggest using "3y" or "2y" in the URL wildcard rather than "3-year" or "2-year" as this will be consistent with existing timespan wildcards for seasonal flu (6m, 2y, 3y, 12y) and for ncov (1m, 2m, 6m, all-time). I'd suggest doing a 2 year target rather than a 3 year target just because there seems to be well sufficient sequence counts in GISAID to pull >3000 genomes for a 2 year span for H5N1. If I look now, I see 5571 H5N1 viruses collected from 2022-04-22 to today. I moved the wildcard dictionary parameters from being all in one-line to being separated by subtype to improve readability.
This commit pulls in changes on master branch that were not present on 2y branch
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Thank you @trvrb for working on this! This looks good to me. Please go ahead and merge! |
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This is mostly @lmoncla's work to implement a new
2yvsall-timewildcard to specify the timespan for individual build targets. This allows a much larger fraction of recent H5N1 sequences to make it into the final subsampled analysis.I had run a version of this AWS using the
h5nx-2-year-testbranch. The results of this run are available on staging with URLS like:Everything here seemed to be in order. However, I couldn't just merge
h5nx-2-year-testintomasteras there were a conflicts due to PR #12 and other work onmaster. To compensate I manually updated this PR branch2y-build-targetsto bring it up to speed withmasterin commit 7549b7d.I tested merging
2y-build-targetsintomasterlocally and it went smoothly with just a copy small resolutions during the merge.@lmoncla: if this looks good to you, I'm happy to help with the merge.