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fix export of strandedness #1211

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merged 4 commits into from
May 25, 2023
Merged

fix export of strandedness #1211

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31f0b26
fix export of strandedness
rneher May 12, 2023
744343b
fix strandedness test
May 12, 2023
03ef91b
fix export v1 to be compatible with new translate
j23414 May 12, 2023
4f4075f
add to changelog
rneher May 13, 2023
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2 changes: 2 additions & 0 deletions CHANGES.md
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Expand Up @@ -6,7 +6,9 @@

* CI: Add a Github action to test augur on 8 Nextstrain pathogen workflows using example data. [#1217][] (@corneliusroemer)
* parse: Denote required arguments including `--fields`, `--output-sequences`, and `--output-metadata`. [#1228][] (@huddlej)
* Fix export of the `strand` attribute of gene annotations. Previously, features on the negative strand were not annotated as such since the code assumed that the `strand` attribute was boolean instead of `[-1, +1]`. [#1211] @rneher and @j23414.

[#1211]: https://github.com/nextstrain/augur/pull/1211
[#1217]: https://github.com/nextstrain/augur/pull/1217
[#1228]: https://github.com/nextstrain/augur/pull/1228

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2 changes: 1 addition & 1 deletion augur/export_v1.py
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Expand Up @@ -176,7 +176,7 @@ def process_annotations(node_data):
annotations[name] = {
"start": info["start"]-1,
"end": info["end"],
"strand": 0 if info["strand"] == "-" else 1
"strand": -1 if info["strand"] == "-" else 1
}
return annotations

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2 changes: 1 addition & 1 deletion augur/translate.py
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Expand Up @@ -397,7 +397,7 @@ def run(args):
'type':feat.type,
'start':int(feat.location.start)+1,
'end':int(feat.location.end),
'strand': '+' if feat.location.strand else '-'}
'strand': {+1:'+', -1:'-', 0:'?', None:None}[feat.location.strand]}
if is_vcf: #need to add our own nuc
annotations['nuc'] = {'seqid':args.reference_sequence,
'type':feat.type,
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