DRAFT: add 'gene' feature capture when reading genbank files #1435
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## master #1435 +/- ##
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+ Coverage 68.66% 68.70% +0.03%
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Files 69 69
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Branches 1851 1866 +15
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+ Hits 5187 5227 +40
- Misses 2089 2098 +9
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| @@ -432,6 +434,21 @@ def _read_genbank(reference, feature_names): | |||
| if fname and (feature_names is None or fname in feature_names): | |||
| features[fname] = feat | |||
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| if feat.type=='gene': | |||
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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"?
Another is to expose this as a command line argument to augur.
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
Description of proposed changes
In response to nextstrain/rsv#55 (comment), adds a 'gene' feature capture when reading GenBank files.
Please feel free to commit changes to this branch, this initial commit was a draft.
We should add a test of some sort to make sure this works as expected, perhaps in augur/tests/io?
The potential benefit of this functionality is to simplify the newreference.py script for Nextstrain gene tree builds.
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