Improve ingest for Andersen lab/SRA sequences #114
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Replace invalid characters with `_` to match iqtree¹ so augur tree will not modify strain names and cause a mismatch between the tree and the alignment FASTA.² Keeps the previous removal of whitespace in place to ensure that the previous valid strain names do not change. ¹ <https://github.com/iqtree/iqtree2/blob/74da454bbd98d6ecb8cb955975a50de59785fbde/utils/tools.cpp#L607> ² <#113>
Use the augur.curate.parse_genbank_location function to parse the
country field since we've now seen an example of it formatted as
the GenBank geolocation format ("USA:OR") in the SRA data.¹
¹ <#113>
These sequences are likely from the recalled cat food in Oregon, which is raw turkey. <https://apps.oregon.gov/oregon-newsroom/OR/ODA/Posts/Post/morasch-meats-voluntary-recall-feline-raw-pet-food-hpai>
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Locally tested the NCBI ingest and diffed output with prod metadata. There was a total of 446 record changes. Most were expected geolocation and host updates, with only 3 strain name changes:
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I'm confident in these changes, so I'm going to merge and re-run the workflows. Post-merge reviews are always welcome! |
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Description of proposed changes
Improve ingest for Andersen lab/SRA sequences to avoid unexpected strain name modifications in the phylogenetic workflow:
Includes updates to geolocation rules, host, and annotations for data issues that I noticed during testing.
Related issue(s)
Resolves #113
Checklist