TaxonKit v0.16.0

Changes

• TaxonKit v0.16.0

  • taxonkit create-taxdump:

    • TaxIds are generated from the hash value of "rank+taxon_name", this allowed duplicated names with different ranks (common in GTDB). #92.

  • taxonkit taxid-changelog/create-taxdump:

    • Add notes about the possible error records in taxid-changelog built from taxonomic data created by create-taxdump. #91

    • Dont't worry, a single version of taxonomic data created by taxonkit create-taxdump has no problem, it's just the changelog might not be perfect.

      $ taxonkit taxid-changelog -h
      Create TaxId changelog from dump archives
      
      Attention:
        1. This command was originally designed for NCBI taxonomy, where the the TaxIds are stable.
        2. For other taxonomic data created by "taxonkit create-taxdump", e.g., GTDB-taxdump,
          some change events might be wrong, because
           a) There would be dramatic changes between the two versions.
           b) Different taxons in multiple versions might have the same TaxIds, because we only
              check and eliminate taxid collision within a single version.
           So a single version of taxonomic data created by "taxonkit create-taxdump" has no problem,
           it's just the changelog might not be perfect.
      
      $ taxonkit create-taxdump -h
      Attention:
        3. We only check and eliminate taxid collision within a single version of taxonomy data.
           Therefore, if you create taxid-changelog with "taxid-changelog", different taxons
           in multiple versions might have the same TaxIds and some change events might be wrong.
      
           So a single version of taxonomic data created by "taxonkit create-taxdump" has no problem,
           it's just the changelog might not be perfect.
      

  • taxonkit lca:

    • new flag -K/--keep-invalid: print the query even if no single valid taxid left. #89

Please cite

Shen, W., Ren, H., TaxonKit: a practical and efficient NCBI Taxonomy toolkit,
Journal of Genetics and Genomics, https://doi.org/10.1016/j.jgg.2021.03.006

Links

Tips

• run taxonkit version to check update !!!
• run taxonkit genautocomplete to update Bash completion !!!

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