get-gtdb refactor - Githubissues

bokulich-lab / RESCRIPt

REference Sequence annotation and CuRatIon Pipeline

BSD 3-Clause "New" or "Revised" License

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get-gtdb refactor #169

Closed mikerobeson closed 5 months ago

mikerobeson commented 6 months ago

Fixes #167 and #168.

This refactor:

File parsing is different.
- We now pull taxonomy from the FASTA files directly, not the taxonomy files.
Download Options:
- GTDB SSU Species Representatives, as we've been doing
  - Both
  - Bacteria
  - Archaea
- Non-species representative GTDB SSUs
- Contains all Bacteria and Archaea that have passed GTDBs QA/QC But are not clustered into species representatives.

To do:

[x] update test code
[x] break up code into simpler functions where possible.