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DRAFT: add 'gene' feature capture when reading genbank files #1435
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To reduce the chances of this introducing unexpected changes to current usage, I'd suggest an approach where we only use 'gene' features if the corresponding 'CDS' feature doesn't exist. There's a few different ways to implement this, but the simplest may be to use an extra loop through
gb.features
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Continuing this discussion based on nextstrain/rsv#55 (comment):
Theoretically CDSs are what we want, but we have GenBank files which use "gene" instead. I can't think of a situation where we want to extract both from the same genbank reference¹. One option is to look for 'gene' only if no CDSs are found. Another is to expose this as a command line argument to augur.
¹ I'm sure there are exceptions to this, in which case I think the onus is on the user to edit the GenBank file upstream of Augur.
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Is this something where we need to poll users to vote for "CDS" or "gene"? Or it sounds like we're pretty sure it's "CDS"?
Ah, I could get behind having a command line argument
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We're sure we want to use CDS, this is what we're moving towards as only CDSes allow complex annotations like ribosomal slippage etc. Nextclade v3 uses CDS moving forward, we've made similar changes for auspice