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De-duplicate NCBI strain #79

Merged
merged 2 commits into from
Jul 23, 2024
Merged

De-duplicate NCBI strain #79

merged 2 commits into from
Jul 23, 2024

Commits on Jul 22, 2024

  1. ingest/andersen-lab: dedup by strain name 

    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.
    @joverlee521
    joverlee521 committed Jul 22, 2024
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  2. ingest/ncbi: Dedup joined-ncbi data 

    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.
    @joverlee521
    joverlee521 committed Jul 22, 2024
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