shenwei356/taxonkit issues and pull requests

#90 - some taxid that have taxonomy on ncbi but taxonkit not found or not complete

Issue - State: open - Opened by weiguanyue 11 months ago - 1 comment

#89 - Include LCA queries in output even when all taxids are skipped

Issue - State: closed - Opened by standage 12 months ago - 3 comments

#88 - [Feature Request] Fuzzy name searching with name2taxid

Issue - State: open - Opened by jolespin about 1 year ago

#87 - Search equivalent names with name2taxid?

Issue - State: open - Opened by alvanuffelen about 1 year ago - 2 comments

#86 - taxonkit equivalent of diamond blastx plus megan blast2lca

Issue - State: open - Opened by avilella about 1 year ago - 3 comments

#85 - ranks skipped in certain GTDB lineages

Issue - State: closed - Opened by ggavelis over 1 year ago - 2 comments

#84 - Filter duplicate taxIDs by order/class?

Issue - State: closed - Opened by philippbayer over 1 year ago - 3 comments
Labels: new feature

#83 - kraken2 report to mpa with counts

Issue - State: closed - Opened by motroy over 1 year ago - 2 comments

#82 - How to add the corresponding taxonomic level prefix based on the taxonomy name?

Issue - State: closed - Opened by YeGuoZJU over 1 year ago - 6 comments

#81 - An error occurs when running the latest version

Issue - State: closed - Opened by weiguanyue over 1 year ago - 5 comments

#80 - Possible issue with `filter --save-predictable-norank` and merged taxids

Issue - State: closed - Opened by standage over 1 year ago - 2 comments
Labels: bug

#79 - taxonkit reformat taxid 0 not found

Issue - State: closed - Opened by Krasnopeev over 1 year ago - 2 comments

#78 - taxid-changelog: support gzip-compressed dump files for saving space

Issue - State: closed - Opened by shenwei356 over 1 year ago - 1 comment
Labels: enhancement

#77 - Placeholder for Clade rank (reformat)

Issue - State: closed - Opened by poursalavati over 1 year ago - 4 comments

#76 - "Error: Invalid taxonomic rank: realm" when making Diamond db of IMG/VR dataset

Issue - State: closed - Opened by poursalavati over 1 year ago - 5 comments

#75 - taxonkit lca gives error `[ERRO] bufio.Scanner: token too long' sometimes

Issue - State: closed - Opened by taylorreiter over 1 year ago - 4 comments
Labels: bug

#74 - Feature request: accession2taxid

Issue - State: closed - Opened by stas-malavin over 1 year ago - 2 comments

#73 - build(deps): bump golang.org/x/sys from 0.0.0-20210510120138-977fb7262007 to 0.1.0

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#72 - Feature request: report specific lineage ranks

Issue - State: closed - Opened by soungalo over 1 year ago - 1 comment

#71 - modification of the dmp files?

Issue - State: closed - Opened by nick-youngblut almost 2 years ago - 2 comments

#70 - Error with makeblastdb using GTDB taxonkit create-taxdump taxid.map

Issue - State: closed - Opened by BenjaminJPerry almost 2 years ago - 4 comments

#69 - Error rush: invalid option -- 'j'

Issue - State: closed - Opened by Metag3nOmics almost 2 years ago - 12 comments

#68 - Error in list method

Issue - State: closed - Opened by Maryam-Haghani about 2 years ago - 10 comments
Labels: bug, bug?

#67 - Create-taxdump not generating subspecies

Issue - State: closed - Opened by Lucas-Maciel about 2 years ago - 4 comments
Labels: tutorial

#66 - panic: runtime error: index out of range [4] with length 4

Issue - State: closed - Opened by Summer0lhl about 2 years ago - 1 comment
Labels: bug?

#65 - Sequence names starting with "Sp_"

Issue - State: closed - Opened by snayfach about 2 years ago - 5 comments

#64 - taxonkit reformat 如何显示kingdom 信息

Issue - State: closed - Opened by zhaolei6116 about 2 years ago - 4 comments
Labels: enhancement

#63 - Trouble creating taxdump after using reformat

Issue - State: closed - Opened by Midnighter over 2 years ago - 6 comments

#62 - Is it expected to have different output from reformat depending on whether the input are only tax IDs or a lineage table?

Issue - State: closed - Opened by Midnighter over 2 years ago - 2 comments

#61 - create-taxdump: accepts arbitrary ranks. #60

Pull Request - State: closed - Opened by shenwei356 over 2 years ago

#60 - create-taxdump: accepts arbitrary ranks

Issue - State: closed - Opened by shenwei356 over 2 years ago - 1 comment

#59 - taxids created with `create-taxdump` skip numbers

Issue - State: open - Opened by apcamargo over 2 years ago - 2 comments

#58 - Make create-taxdump parse classes correctly

Pull Request - State: closed - Opened by apcamargo over 2 years ago

#57 - `create-taxdump` ignores the class rank

Issue - State: closed - Opened by apcamargo over 2 years ago - 5 comments

#56 - TODO: new command to create taxdump files for MAG genome collections

Issue - State: closed - Opened by shenwei356 over 2 years ago - 15 comments

#55 - When converting 'taxid' into full taxonomy from prot.accession2taxid , the program terminated after an error is reported

Issue - State: closed - Opened by Neal050617 almost 3 years ago - 10 comments
Labels: bug?

#54 - Taxonkit Bash-completion terminal error

Issue - State: closed - Opened by divya1srv almost 3 years ago - 1 comment

#53 - [Question] How to get specific taxonomic fields (not full taxonomy string) from a list of taxon identifiers?

Issue - State: closed - Opened by jolespin almost 3 years ago - 5 comments

#52 - "out of range" error for Reformat on long taxonomic strings

Issue - State: closed - Opened by mycowx almost 3 years ago - 2 comments

#51 - Taxonkit list tabular output

Issue - State: closed - Opened by mweberr almost 3 years ago - 2 comments

#50 - fixes typos with strain

Pull Request - State: closed - Opened by tolot27 about 3 years ago - 1 comment

#49 - [Question] Get all species-level taxon ids for organism

Issue - State: closed - Opened by jolespin over 3 years ago - 3 comments

#48 - About the special taxonID search

Issue - State: closed - Opened by hansir8 over 3 years ago - 2 comments

#47 - Update benchmarks

Issue - State: open - Opened by apcamargo over 3 years ago

#46 - How to Extract GenBank 15-taxon format abbreviated lineage

Issue - State: open - Opened by yxj17173 over 3 years ago
Labels: new feature

#45 - Convertion between taxonomic profiling tables with different taxonomy dump file versions?

Issue - State: closed - Opened by shenwei356 over 3 years ago - 2 comments

#44 - Can I filter taxids using a set of taxids?

Issue - State: closed - Opened by Lix1993 over 3 years ago - 2 comments

#43 - Can I get kingdom using taxonkit?

Issue - State: closed - Opened by Lix1993 over 3 years ago - 2 comments

#42 - Taxon taxid reassigned with reformat

Issue - State: closed - Opened by standage over 3 years ago - 11 comments
Labels: enhancement, new feature

#41 - R bindings for taxonkit?

Issue - State: closed - Opened by johanneswerner over 3 years ago - 4 comments

#40 - Unsure about usage of --pseudo-strain

Issue - State: closed - Opened by standage almost 4 years ago - 3 comments

#39 - reformat: add placeholder for strain?

Issue - State: closed - Opened by shenwei356 almost 4 years ago - 1 comment

#38 - Difference between `--list-order` and `--list-ranks` unclear

Issue - State: closed - Opened by standage almost 4 years ago - 3 comments

#37 - Possible bug with taxonkit filter --black-list

Issue - State: closed - Opened by standage almost 4 years ago - 12 comments

#36 - Unnecessary stdin check for taxonkit filter?

Issue - State: closed - Opened by standage almost 4 years ago - 4 comments

#35 - Inconsistent "taxonkit reformat" output for 446045

Issue - State: closed - Opened by standage about 4 years ago - 3 comments
Labels: bug

#34 - accession numbers not found

Issue - State: closed - Opened by srosales712 over 4 years ago - 1 comment

#33 - Refactor: daemon + IPC

Issue - State: closed - Opened by shenwei356 over 4 years ago - 1 comment
Labels: new feature

#32 - filtering ranks

Issue - State: closed - Opened by shenwei356 over 4 years ago - 11 comments
Labels: new feature

#31 - taxonkit reformat omits species for some species taxids

Issue - State: closed - Opened by Shellfishgene over 4 years ago - 2 comments

#30 - JSON output is malformed when running `taxonkit list`

Issue - State: closed - Opened by standage over 4 years ago - 4 comments

#29 - duplicate taxid from name2taxid

Issue - State: closed - Opened by slaperriere over 4 years ago - 5 comments
Labels: bug?

#28 - [ERRO] lineage-field (2) out of range (1)

Issue - State: closed - Opened by nick-youngblut almost 5 years ago - 1 comment

#27 - Why require delnodes.dmp and merged.dmp?

Issue - State: closed - Opened by nick-youngblut about 5 years ago - 5 comments

#26 - no lineage info when using custom nodes+names dmp

Issue - State: closed - Opened by nick-youngblut about 5 years ago - 2 comments

#25 - how to use taxid-changelog

Issue - State: closed - Opened by Phylloxera over 5 years ago - 4 comments

#24 - taxid-changelog bug: 10842

Issue - State: closed - Opened by shenwei356 over 5 years ago - 2 comments
Labels: bug

#23 - taxonkit taxid-changeloge: order error of changes in one taxid

Issue - State: closed - Opened by shenwei356 over 5 years ago
Labels: bug

#22 - new cmd: taxid-changelog

Pull Request - State: closed - Opened by shenwei356 over 5 years ago

#21 - autocompletion inside Tmux

Issue - State: closed - Opened by matrs over 5 years ago

#20 - Ranks of interest for taxonkit lineage

Issue - State: closed - Opened by johanneswerner over 5 years ago - 4 comments

#19 - no taxonomy for "1458427"

Issue - State: closed - Opened by nick-youngblut almost 6 years ago - 3 comments
Labels: enhancement

#18 - Adding and removing nodes

Issue - State: closed - Opened by lskatz about 6 years ago - 2 comments

#17 - $TAXONKIT_DB variable for file locations?

Issue - State: closed - Opened by tseemann about 6 years ago - 2 comments
Labels: enhancement

#16 - Export newick tree?

Issue - State: closed - Opened by boulund about 6 years ago - 1 comment

#15 - Now in Brew

Issue - State: closed - Opened by tseemann about 6 years ago - 4 comments

#14 - taxonkit reformat erro :panic: runtime error: invalid memory address or nil pointer dereference

Issue - State: closed - Opened by wfgui over 6 years ago - 4 comments

#13 - add installation script for unix machines

Pull Request - State: closed - Opened by IsmailM over 6 years ago - 1 comment

#12 - citation

Issue - State: closed - Opened by IsmailM over 6 years ago - 4 comments

#11 - line-buffered output

Issue - State: closed - Opened by tolot27 over 6 years ago - 2 comments

#10 - obsolete taxid check

Issue - State: closed - Opened by msaavedrat over 6 years ago - 6 comments
Labels: enhancement

#9 - taxonkit Synonyms

Issue - State: closed - Opened by msaavedrat almost 7 years ago
Labels: new feature

#8 - output taxid for certain rank or complete lineage

Issue - State: closed - Opened by tolot27 almost 7 years ago - 13 comments

#7 - `taxonkit lineage` stalls if taxID = 1

Issue - State: closed - Opened by nick-youngblut almost 7 years ago - 1 comment
Labels: bug

#6 - format options in lineage command

Issue - State: closed - Opened by tolot27 almost 7 years ago - 5 comments

#5 - reformat should support tab characters in format string

Issue - State: closed - Opened by tolot27 almost 7 years ago - 1 comment

#4 - No output for leaf nodes of the taxonomy

Issue - State: closed - Opened by ialbert over 7 years ago - 7 comments
Labels: bug

#3 - Taxon ID instead of names in lineage

Issue - State: closed - Opened by AsmaTahir over 7 years ago - 2 comments

#2 - Functionality request

Issue - State: closed - Opened by dawnmy over 7 years ago

#1 - There are so many ranks

Issue - State: closed - Opened by shenwei356 almost 8 years ago - 5 comments

GitHub / shenwei356/taxonkit issues and pull requests