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 !!!

OS	Arch	File, 中国镜像	Download Count
Linux	64-bit	taxonkit_linux_amd64.tar.gz, 中国镜像
Linux	arm64	taxonkit_linux_arm64.tar.gz, 中国镜像
macOS	64-bit	taxonkit_darwin_amd64.tar.gz, 中国镜像
macOS	arm64	taxonkit_darwin_arm64.tar.gz, 中国镜像
Windows	64-bit	taxonkit_windows_amd64.exe.tar.gz, 中国镜像

TaxonKit v0.15.1

Changes

• TaxonKit v0.15.1
  • taxonkit name2taxid:
    • remove the restriction of name types. #87
  • added a new tutorual: Mapping old species names to new ones.

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 !!!

OS	Arch	File, 中国镜像	Download Count
Linux	64-bit	taxonkit_linux_amd64.tar.gz, 中国镜像
Linux	arm64	taxonkit_linux_arm64.tar.gz, 中国镜像
macOS	64-bit	taxonkit_darwin_amd64.tar.gz, 中国镜像
macOS	arm64	taxonkit_darwin_arm64.tar.gz, 中国镜像
Windows	64-bit	taxonkit_windows_amd64.exe.tar.gz, 中国镜像

TaxonKit v0.15.0

Changes

• TaxonKit v0.15.0
  • taxonkit reformat:
    • For lineages with more than one node, if it fails to query TaxId with the parent-child pair, use the last child only. #82
    • The flag -T/--trim also does not add the prefix for missing ranks lower than the current rank. #82
    • New flag -s/--miss-rank-repl-suffix to set the suffix for estimated taxon names. #85

TaxonKit v0.14.2

Changes

• TaxonKit v0.14.2
  • taxonkit filter:
    • fix checking merged/deleted/not-found taxids. #80
  • taxonkit lca:
    • add a new flag -b/--buffer-size to set the size of the line buffer. #75
    • fix typos: --separater -> --separater, the former is still available for backward compatibility.
  • taxonkit reformat:
    • output compatible format for TaxIds not found in the database. #79
  • taxonkit taxid-changelog:
    • support gzip-compressed taxdump files for saving space. #78

TaxonKit v0.14.1

Changes

• TaxonKit v0.14.1
  • taxonkit reformat:
    • The flag -S/--pseudo-strain does not require -F/--fill-miss-rank now.
    • For taxa of rank >= species, {t}, {S}, and T outputs nothing when using -S/--pseudo-strain.

TaxonKit v0.14.0

Changes

• TaxonKit v0.14.0
  • taxonkit create-taxdump:
    • save taxIds in int32 instead of uint32, as BLAST and DIAMOND do. #70
  • taxonkit list:
    • do not skip visited subtrees when some of the given taxids are descendants of others. #68
  • taxonkit:
    • when environment variable TAXONKIT_DB is set, explicitly setting --data-dir will override the value of TAXONKIT_DB.

TaxonKit v0.13.0

Changes

• TaxonKit v0.13.0
  • taxonkit reformat:
    • add a new placeholder {K} for rank kingdom. #64
    • do not panic for invalid TaxIds, e.g., the column name, when using -I--taxid-field.
  • taxonkit create-taxdump:
    • fix merged.dmp and delnodes.dmp. Thanks to @apcamargo ! gtdb-taxdump/issues/2.
    • fix bug of handling non-GTDB data when using -A/--field-accession and no rank names given:
      the colname of the accession column would be treated as one of the ranks, which messed up all the ranks.
    • fix the default option value of --field-accession-re which wrongly remove prefix like Sp_. #65
  • taxonkit list:
    • fix warning message of merged taxids.

TaxonKit v0.12.0

Changes

• TaxonKit v0.12.0
  • taxonkit create-taxdump:
    • accepts arbitrary ranks #60
    • better handle of taxa with same names.
    • many flags changed.

TaxonKit v0.12.0-alpha

Changes

• taxonkit create-taxdump:
  • accepts arbitrary ranks #60
  • better handle of taxa with same names.
  • many flags changed.

TaxonKit v0.11.1

Changes

• TaxonKit v0.11.1
  • taxonkit create-taxdump: fix bug of missing Class rank, contributed by @apcamargo. The flag --gtdb was not effected. #57