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peterjc / thapbi-pict

Tree Health and Plant Biosecurity Initiative - Phytophthora ITS1 Classifier Tool
https://thapbi-pict.readthedocs.io/
MIT License
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Clarify incremental updates to Oomycota_ITS1_obs.fasta #503

Closed peterjc closed 5 months ago

peterjc commented 2 years ago

The current 2022-08-17_ITS1_Oomycota_obs.fasta file was built against v0.12.5 and included in v0.12.6 onwards.

Right now with v0.12.9 repeating the procedure (with the DB including those sequences) results in shorter unknowns.fasta and empty file of observed left-extensions to be included.

Essentially we need to either make a temp DB without the old yyyy-mm-dd_ITS1_Oomycota_obs.fasta entries, or update yyyy-mm-dd_ITS1_Oomycota_obs.fasta incrementally.

Note that yyyy-mm-dd_ITS1_Oomycota_obs.fasta can lose entries as things are added to the w32 or curated files, as well as gain entries as we sequence more samples.

peterjc commented 8 months ago

Note cacb5ce4f8ba0f06b6be10d97c9f221216c54162 dropped the date prefixes.