phylogenetic: include the edited variants of the P gene in the reference #35
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Handles slippage in P gene related to nextstrain/augur#1901 (comment) |
victorlin
requested changes
Oct 10, 2025
phylogenetic/defaults/reference.gb
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| gene 1916..2426 | ||
| /gene="I" | ||
| CDS 1916..2431 | ||
| CDS join(1916..2380,2377..2426) |
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Tested with nextstrain/augur#1901. P gene looks good now, but there's a new error with I gene:
$ nextstrain build --augur=/path/to/local/nextstrain/augur phylogenetic results/global/aa_muts.json --rerun-incomplete
ERROR: Reference file 'defaults/reference.gb' failed validation:
'I' has length 515 which is not a multiple of 3.
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Thanks, fixup in 4018a3c based on what I can see in Geneious and genbank annotation
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I'm not familiar with the reasoning, but augur translate now succeeds in the test command so this looks good to me!
victorlin
approved these changes
Oct 10, 2025
Similar to the fix in the Nextclade workflow. * https://github.com/nextstrain/mumps/blame/41654ec8e601f4669146d4c3ac1834ae7f74c12f/nextclade/defaults/genome/reference.gb#L54 1. Align the nextclade genome reference and the phylogenetic genome reference 2. Compare P and I CDS and gene annotations 3. Glance at the annotated translations and the automatic translations
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Description of proposed changes
Similar to the fix in the Nextclade workflow
Basically changing from original:
to:
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