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augur curate transform-strain-name #1486

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

augur curate transform-strain-name #1486

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

Verify the strain name pattern and use a backup field value if the strain name pattern does not match. This subcommand was more relevant when augur did not have the --metadata-id-column option and the strain column was required to be non-empty and unique.

Description

augur curate transform-strain-name can start from transform-strain-names from ingest.

Consider #1515 or leave as a future TODO.
@joverlee521 joverlee521 mentioned this issue Jun 24, 2024
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@genehack genehack self-assigned this Jul 1, 2024
genehack added a commit that referenced this issue Jul 2, 2024
@genehack
cp ingest/transform-strain-names augur/augur/curate/transform_strain_…
90ac28b 
…name.py [#1486]
genehack added a commit that referenced this issue Jul 2, 2024
@genehack
Port translate-strain-name into augur curate style [#1486]
146865f 
* Convert script over to expected sub-cmd style
* Add type hints throughout
* Add tests
@genehack genehack mentioned this issue Jul 2, 2024
Merged
2 tasks
genehack added a commit that referenced this issue Jul 2, 2024
@genehack
Update CHANGES [#1486]
455a76b
genehack added a commit that referenced this issue Jul 2, 2024
@genehack
Port translate-strain-name into augur curate style [#1486]
ff2faf9 
* Convert script over to expected sub-cmd style
* Add type hints throughout
* Add tests
genehack added a commit that referenced this issue Jul 2, 2024
@genehack
Update CHANGES [#1486]
d33556c
@joverlee521 joverlee521 mentioned this issue Jul 2, 2024
Closed
genehack added a commit that referenced this issue Jul 2, 2024
@genehack
Merge pull request #1514 from nextstrain/port-xform-strain-name-1486
9447c66 
Port `ingest/transform-strain-names` to `augur curate transform-strain-name` [#1486]
@genehack genehack closed this as completed Jul 2, 2024
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