TaxonKit v0.7.2

Changelog

• TaxonKit v0.7.2
  • taxonkit lineage:
    • new flag -R/--show-lineage-ranks for appending ranks of all levels.
    • reduce memory occupation and slightly speedup.
  • taxonkit filter:
    • flag -E/--equal-to supports multiple values.
    • new flag -n/--save-predictable-norank: do not discard some special ranks without order when using -L, where rank of the closest higher node is still lower than rank cutoff.
  • taxonkit reformat:
    • new placeholder {t} for subspecies/strain, {T} for strain. Thanks @wqssf102 for feedback.
    • new flag -S/--pseudo-strain for using the node with lowest rank as strain name, only if which rank is lower than "species" and not "subpecies" nor "strain".

TaxonKit v0.7.1

Changelog

• TaxonKit v0.7.1
  • taxonkit filter:
    • disable unnecessary stdin check when using flag --list-order or --list-ranks. #36
    • better handling of black list, empty default value: "no rank" and "clade". And you need use -N/--discard-noranks to explicitly filter out "no rank", "clade". #37
    • update help message. Thanks @standage for improve this command! #38

TaxonKit v0.7.0

Changes

• TaxonKit v0.7.0
  • taxonkit: 2-3X faster taxonomy data loading.
  • new command taxonkit filter: filtering taxIDs by taxonomic rank range. #32
  • new command taxonkit lca: Computing lowest common ancestor (LCA) for taxIDs.
  • taxonkit reformat:
    • new flag -P/--add-prefix: add prefixes for all ranks, single prefix for a rank is defined by flag --prefix-X, where X may be k, p, c, o, f, s, S.
    • new flag -T/--trim: do not fill missing rank lower than current rank.
  • taxonkit list: do not duplicate root node.

TaxonKit v0.6.2

• TaxonKit v0.6.2
  • taxonkit reformat -F: fix taxids of abbreviated lineage containing names shared by different taxids. #35

TaxonKit v0.6.1

• TaxonKit v0.6.1
  • taxonkit lineage:
    • new flag -n/--show-name for appending scientific name.
    • new flag -L/--no-lineage for hide lineage, this is for fast retrieving names or/and ranks.
  • taxonkit reformat:
    • fix flag -F/--fill-miss-rank.
    • discard order restriction of rank symbols.

TaxonKit v0.6.0

Changes

• TaxonKit v0.6.0
  • taxonkit list:
    • check merged and deleted taxids.
    • fix bug of json output. #30
  • taxonkit name2taxid: new flag -s/--sci-name for limiting to searching scientific names. #29
  • taxonkit version: make checking update optional

TaxonKit v0.5.0

• TaxonKit v0.5.0
  • taxonkit: requiring delnodes.dmp and merged.dmp.
  • taxonkit lineage: detect deleted and merged taxids now. #19
  • taxonkit list/name2taxid: add short flag -r for --show-rank, -n for --show-name.

TaxonKit v0.4.3

Changelog

• TaxonKit v0.4.3
  • taxonkit taxid-changelog: rewrite logic, fix bug and add more change types

TaxonKit v0.4.2

Changelog

• TaxonKit v0.4.2
  • taxonkit taxid-changelog: change output of ABSORB, do not merged into one record for changes in different versions.

v0.4.1

• TaxonKit v0.4.1
  • taxonkit taxid-changelog:
    • add fields: name and rank.
    • and fix sorting bug.
    • detailed lineage change status.