Get ready for new NCBI Taxonomy

[crosenth]

New taxonomy coming soon:

https://ncbiinsights.ncbi.nlm.nih.gov/2024/06/04/changes-ncbi-taxonomy-classifications/

taxit new_database has been added to the GHA test workflow and subscribed the NCBI Insights blog for updates to come

[nach00gar]

Last night, files from ncbi were updated adding the domain rank. An update is required.

https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/

[crosenth]

Thank you for the heads up!

[crosenth]

@dhoogest: https://ncbiinsights.ncbi.nlm.nih.gov/2025/02/27/new-ranks-ncbi-taxonomy/

[crosenth]

@nach00gar - v0.11.0 is out and should close this Issue, let me know

[crosenth]

New celllular_root and acellular_root

https://ncbiinsights.ncbi.nlm.nih.gov/2025/02/27/new-ranks-ncbi-taxonomy/#more-14432

v0.11.0...v0.11.1

[yeemey]

Has 'realm' been added as well? I used taxit v0.11.1 taxit taxtable and got the following error when using taxdmp downloaded on 5/20/25:

Traceback (most recent call last):
  File "/usr/local/bin/taxit", line 8, in <module>
    sys.exit(main())
             ~~~~^^
  File "/usr/local/lib/python3.13/site-packages/taxtastic/scripts/taxit.py", line 51, in main
    return action(arguments)
  File "/usr/local/lib/python3.13/site-packages/taxtastic/subcommands/taxtable.py", line 160, in action
    sorted_ranks = sorted(all_ranks, key=order_ranks(tax.ranks[::-1]))
  File "/usr/local/lib/python3.13/site-packages/taxtastic/subcommands/taxtable.py", line 73, in _inner
    return (ref_ranks.index(rank), 0)
            ~~~~~~~~~~~~~~~^^^^^^
ValueError: 'realm' is not in list

[dhoogest]

@yeemey yep there are a few nodes with that rank, which doesn't appear in the 'ranks' table (see related #175). It's possible NCBI will self-resolve, but this does re-raise question about how to make taxtastic more resilient during change periods