CHANGELOG.md

• TaxonKit v0.19.0
  • new command taxonkit reformat2: Reformat lineage in chosen ranks, allowing more ranks than 'reformat'
  • taxonkit reformat:
    • Fix -T/--trim which did not work for -r/--miss-rank-repl. #106
• TaxonKit v0.18.0
  • taxonkit reformat:
    • Add a placeholder for rank "realm", "{r}", which is common in Virus taxonomy like ictv. #102
  • taxonkit name2taxid:
    • Show warning for names with multiple taxids. #103
• TaxonKit v0.17.0
  • taxonkit filter:
    • Fix keeping taxids with a rank of "no rank" or "clade". #97
  • taxonkit list:
    • Accept input TaxIds from stdin/files, not just the flag --ids. #93
  • taxonkit name2taxid:
    • Add support of fuzzy match with -f/--fuzzy. #88
  • taxonkit profile2cami:
    • Add a new flag -S/--no-sum-up to disable summing up abundances. #99
• 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 lca:
    • new flag -K/--keep-invalid: print the query even if no single valid taxid left. #89
• TaxonKit v0.15.1
  • taxonkit name2taxid:
    • remove the restriction of name types. #87
• 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
  • 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
  • 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
  • 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 give taxids are descendants of others. #68
  • taxonkit:
    • When environment variable TAXONKIT_DB is set, explicitly setting --data-dir will overide the value of TAXONKIT_DB.
• 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
  • taxonkit create-taxdump:
    • accepts arbitrary ranks #60
    • better handle of taxa with same names.
    • many flags changed.
• TaxonKit v0.11.1
  • taxonkit create-taxdump: fix bug of missing Class rank, contributed by @apcamargo. The flag --gtdb was not effected. #57
• TaxonKit v0.11.0
  • new command taxonkit create-taxdump: Create NCBI-style taxdump files for custom taxonomy, e.g., GTDB and ICTV. #56
• TaxonKit v0.10.1
  • taxonkit cami2-filter: fix option --show-rank which did not work in v0.10.0.
• TaxonKit v0.10.0
  • new command taxonkit cami2-filter: Remove taxa of given TaxIds and their descendants in CAMI metagenomic profile
  • taxonkit reformat: fix panic for deleted taxid using -F/--fill-miss-rank . #55
• TaxonKit v0.9.0
  • new command taxonkit profile2cami: converting metagenomic profile table to CAMI format
• TaxonKit v0.8.0
  • taxonkit reformat:
    • accept input of TaxIds via flag -I/--taxid-field.
    • accept single taxonomy names.
    • show warning message for TaxIds with the same lineage. #42
    • better flag checking. #40
  • taxonkit lca:
    • slightly speedup.
  • taxonkit genautocomplete:
    • support bash|zsh|fish/powershell
• 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
  • 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
  • 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 reformat -F: fix taxids of abbreviated lineage containing names shared by different taxids. #35
• 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
  • 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: 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
  • taxonkit taxid-changelog: rewrite logic, fix bug and add more change types
• TaxonKit v0.4.2
  • taxonkit taxid-changelog: change output of ABSORB, do not merged into one record for changes in different versions.
• TaxonKit v0.4.1
  • taxonkit taxid-changelog:
    • add fields: name and rank.
    • and fix sorting bug.
    • detailed lineage change status
• TaxonKit v0.4.0
  • new command: taxonkit taxid-changelog: for creating taxid changelog from dump archive
• TaxonKit v0.3.0
  • this version is almost the same as v0.2.5
• TaxonKit v0.2.5
  • add global flag: --line-buffered to disable output buffer. #11
  • replace global flags --names-file and --nodes-file with --data-dir, also support environment variable TAXONKIT_DB. #17
  • taxonkit reformat: detects lineages containing unofficial taxon name and won't show panic message.
  • taxonkit name2taxid: supports synonyms names. #9
  • taxokit lineage: add flag -r/--show-rank to print rank at another new column.
• TaxonKit v0.2.4
  • taxonkit reformat:
    • more accurate result when using flag -F/--fill-miss-rank to estimate and fill missing rank with original lineage information
    • supporting escape strings like \t, \n, #5
    • outputting corresponding taxids for reformated lineage. #8
  • taxonkit lineage:
    • fix bug for taxid 1 #7
    • add flag -d/--delimiter.
• TaxonKit v0.2.3
  • fix bug brought in v0.2.1
• TaxonKit v0.2.2
  • make verbose information optional #4
• TaxonKit v0.2.1
  • taxonkit list: fix bug of no output for leaf nodes of the taxonomic tree. #4
  • add new command genautocomplete to generate shell autocompletion script!
• TaxonKit v0.2.0
  • add command name2taxid to query taxid by taxon scientific name.
  • lineage, reformat: changed flags and default operations, check the usage.
• TaxonKit v0.1.8
  • taxonkit lineage, add an extra column of lineage in Taxid. #3. e.g.,
  • fix colorful output in windows.
• TaxonKit v0.1.7
  • taxonkit reformat: supports reading stdin from output of taxonkit lineage, reformated lineages are appended to input data.
• TaxonKit v0.1.6
  • remove flag -f/--formated-rank from taxonkit lineage, using taxonkit reformat can archieve same result.
• TaxonKit v0.1.5
  • reorganize code and flags
• TaxonKit v0.1.4
  • add flag --fill for taxonkit reformat, which estimates and fills missing rank with original lineage information
• TaxonKit v0.1.3
  • add command of taxonkit reformat which reformats full lineage to custom format
• TaxonKit v0.1.2
  • add command of taxonkit lineage, users can query lineage of given taxon IDs from file
• TaxonKit v0.1.1
  • add feature of taxonkit list, users can choose output in readable JSON format by flag --json so the taxonomy tree could be collapse and uncollapse in modern text editor.
• TaxonKit v0.1
  • first release