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augur curate parse-genbank-location #1485

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Tracked by #43
joverlee521 opened this issue Jun 24, 2024 · 0 comments
Closed
Tracked by #43

augur curate parse-genbank-location #1485

joverlee521 opened this issue Jun 24, 2024 · 0 comments
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Context

Follow Genbank docs to parse their geo_loc_name field (previously country) into 3 separate geolocation fields: country, division and location.

Description

augur curate parse-genbank-location can start from transform-genbank-location from ingest.
@joverlee521 joverlee521 mentioned this issue Jun 24, 2024
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@genehack genehack self-assigned this Jun 28, 2024
genehack added a commit that referenced this issue Jul 1, 2024
@genehack
cp ingest/transform-genbank-location augur/curate/parse_genbank_locat…
8ecd4eb 
…ion [#1485]
genehack added a commit that referenced this issue Jul 1, 2024
@genehack
Port parse-genbank-location into augur curate style [#1485]
2100393 
* Convert script over to expected sub-command style
* Add `--location-field` argument to preserve back-compat with older
  data files
* Add type hints throughout
* Add tests
genehack added a commit that referenced this issue Jul 1, 2024
@genehack
Update CHANGES [#1485]
975262e
@genehack genehack mentioned this issue Jul 1, 2024
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genehack added a commit that referenced this issue Jul 1, 2024
@genehack
Merge pull request #1508 from nextstrain/parse-gb-loc-1485
a9d1b3a 
Port `translate-genbank-location` to `augur curate parse-genbank-location` [#1485]
@genehack genehack mentioned this issue Jul 2, 2024
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@genehack @joverlee521