Ingest #24
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Ingest #24
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victorlin
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May 5, 2023
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Just to clarify, 342ead8 is copying from nextstrain/dengue#6 which copies from the monkeypox repo in nextstrain/dengue@4b19154 and makes additional changes?
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Haha, yes! I wish there was a simpler way
Future commits will change this to work with zika data
Since the original zika ingest only pulled data from 2013 onward, modify the genbank-url script to only pull data from 2013 onward.
Since Ingest pushes data to a different endpoint, update zika build to pull from the new endpoint. Other modifications from the original described below: Since strains (or isolates) may be re-sequenced resulting in duplicate strain names breaking Nextstrain builds, other pathogen repos (e.g. Monkeypox) had switched to indexing records by GenBank ID instead (`rule wrangle_metdata`) and swapping in the final strain name at the end (`rule final_strain_name`) and Zika was updated accordingly. Other changes include updating the list of dropped strain names to GenBank IDs (where the original strain names moved to comments) and updating the example sequence fasta headers. In addition, added the strain name as a Tip Label dropdown item as discussed in: #25 (comment)
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Rescue some of the original functionality of the zika_upload script from fauna. https://github.com/nextstrain/fauna/blob/master/vdb/zika_upload.py#L14-L30 * Remove monkeypox annotations.tsv * Move strain name, location, and date fixes to annotations.tsv * Match strain names in fauna database * Match locations in fauna database if both region and country names do not match * Match dates in fauna database unless genbank has been updated
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There have been changes to how we add ingest so closing this PR. A new attempt can start from a blank slate. |
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Description of proposed changes
See commit messages.
Related issue(s)
Testing
If reviewer wants to run a local check as documented in ingest/README.md and README.md: