Fetch (optional) root-sequence JSON #1197
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jameshadfield
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This modifies the default workflow to produce the sidecar root-sequence JSON for each build. This is in preparation for nextstrain/auspice#1197 (see there for an explanation of the advantages this JSON gives us)
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this would be quite useful also for nextclade. we could then fetch the root sequence along with the tree and make it work for any of our builds. |
Currently genotypes are unknown for positions without any mutations, as it is through mutations we infer the appropriate values to display. This commit changes the coloring to be grey in such cases, rather than blue/green.
Upon dataset load we now make a request for the "root-sequence" sidecar file. If this request is successful we use the data to color genotypes for which there are no mutations (previously the nt/aa at such positions weren't known)
This switches to getting vic & yam from the nextstrain staging bucket as the root-sequence JSONs weren't present on the data bucket
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Merging after rebasing onto master & retesting |
jameshadfield
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This modifies the default workflow to produce the sidecar root-sequence JSON for each build. See nextstrain/auspice#1197 for the functionality this file gives Auspice.
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Auspice has had a long-standing issue where choosing a genotype for a position where no mutations were observed resulted in an uninformative coloring of the tree. This is because we don't store the ancestral (root) sequence in the dataset JSON and thus rely on mutations to infer it.
Upon dataset load we now make a request for the "root-sequence" sidecar file. If this request is successful we use the data to color genotypes for which there are no mutations. The get-dataset script (which runs for auspice heroku deployments) has been modified to fetch vic & yam from the staging server, as corresponding root-sequence JSONs were present there but not on nextstrain-data.
You can see this in action via https://auspice-root-seq-doeexpnizvfdt.herokuapp.com/flu/seasonal/vic/ha/3y?c=gt-HA2_120 -- notice how the tree starts off with a grey coloring and then once the root-sequence JSON request arrives the coloring updates to show the correct AA (T). Contrast this with https://auspice-root-seq-doeexpnizvfdt.herokuapp.com/flu/seasonal/h3n2/ha/3y?c=gt-HA2_120 for which the root-sequence JSON isn't available.
@emmahodcroft do you have a root-sequence JSON for a TB dataset? Presumably that will be a large JSON and it'd be good to use that for testing to see if there are any issues.