De-duplicate NCBI strain #79
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Resolves #77 It is unclear whether the flagged records listed in the issue are true duplicates or data entry errrors, but the workflow should deduplicate by strain name anyways since we depend on the strain name to match metadata and sequences in the phylogenetic workflow.
I noticed in working through #77 that we do not deduplicate the joined GenBank/Andersen lab SRA data. We only append SRA data if they are not linked to any GenBank records, but there's still a chance that they can share the same strain name. We have not run into any duplicates yet, but adding deduplcation as a precaution.
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Confirmed changes removes the 18 duplicate strain names flagged in #77. |
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Merging before today's automated run |
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Description of proposed changes
De-duplicate records by strain name in both the Andersen lab ingest and the final join of NCBI and Andersen lab data.
This is necessary because we depend on the strain name to match metadata and sequences in the phylogenetic workflow.
Related issue(s)
Resolves #77
Checklist