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yatisht
Stop codons are chopped off in Auspice.json export, ORF8:Q27* wrongly displayed as ORF8:Q27
I spotted this weird mutation ORF8:Q27 which missed the target of the mutation.
https://nextstrain.org/fetch/genome.ucsc.edu/trash/ct/subtreeAuspice1_genome_8534_6af60.json?label=nuc%20mutations:G24410A
It turns out, that it should be a stop codon here ORF8:Q27* so it looks like you remove that * somewhere erroneously, or is this on purpose?
@amkram Please have a look. I think there should have been a "*" as @corneliusroemer points out.
I think that's the web interface not matUtils JSON output -- I'll look into it.
Yep, I was calling a library function that returns '\0' for stop codons, oops -- I will detect that and use '*', thanks for pointing that out!
This will be fixed on our test site pretty soon, but unfortunately this week has the worst timing for our release cycle (code cutoff every 3 weeks, then 1 week testing) so the fix will not appear on our main site until Nov. 16th! In the meantime I hope you can accept "Q27" as an awkward shorthand for "Q27*", sorry. (A back-mutation from stop-codon back to reference would appear as "27Q" I believe, since I'm using the same lib function, but after the fix would be "*27Q".)
Great!
While we're at it, is there a reason Mu hasn't been added to 21H yet, here? Does that matter? Just spotted when I went through the code quickly.
https://github.com/ucscGenomeBrowser/kent/blob/b83116855bd919a0da2b417f07d4473828c94845/src/hg/hgPhyloPlace/treeToAuspiceJson.c#L52
Ah, the reason is that I've fallen behind Nextstrain & WHO letters. Ah, nextclade as well. Thank you for pointing that out!
Yeah, these periodic updates are tedious, been there! Just wanted to point out that you may need to update. I forgot about 21I/J, these are also probably not included yet.