fix: parse source from gff to add nuc annotation
#976
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partially resolves BUG: `augur translate` not faithful to `gff3` standard, can't annotate nucs, which are required. #953
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@@ Coverage Diff @@
## master #976 +/- ##
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- Coverage 59.34% 59.32% -0.02%
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Files 50 50
Lines 6257 6259 +2
Branches 1584 1585 +1
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Hits 3713 3713
- Misses 2283 2285 +2
Partials 261 261
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rneher
approved these changes
Jun 17, 2022
jameshadfield
approved these changes
Jun 21, 2022
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Let's get this merged!
Doesn't make translate fully GFF3 compliant (yet) that's why it's only a partial fix.
I don't think there is such a thing in practice -- see my comment in #953. All of that is for a future PR - this PR works and should be merged.
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partially resolves BUG:
augur translatenot faithful togff3standard, can't annotate nucs, which are required. #953This PR is required to be able to use the GFF3 genemap for the new reference for monkeypox, see nextstrain/mpox#67
Description of proposed changes
Currently, when
augur translateis used with a gff3 genemap as input, nucleotides are not parsed and output into the annotation read in byexport.This means that
gff3is not readily usable as input which is a shame.This PR makes sure that the
sourcefeature is read in and used as basis ofnucannotation.Related issue(s)
Related to #953
Doesn't make translate fully GFF3 compliant (yet) that's why it's only a partial fix.
Testing
Tested locally with mpox, works as expected. Nuc is now output and used by export correctly.
Once this is merged, we can merge nextstrain/mpox#69