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peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
8 stars 2 forks source link

Automate NCBI updates with esearch and efetch #580

Closed peterjc closed 8 months ago

peterjc commented 8 months ago

Uses the NCBI Entrez Direct utilities to script the first part of the DB update process. Had to drop using date prefixed filenames (which was a hassle anyway).

Updating the tests (and worked examples) is still manual.