From dc6190819acdeb05391bb90526a68886d7d78d37 Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Wed, 21 Dec 2022 16:48:10 +0800 Subject: [PATCH] v0.14.1 --- doc/docs/download.md | 31 ++++++++++++++++++------------- doc/docs/tutorial.md | 6 +++--- doc/docs/usage.md | 30 ++++++++++++++++++++---------- 3 files changed, 41 insertions(+), 26 deletions(-) diff --git a/doc/docs/download.md b/doc/docs/download.md index 36db681..597a3a3 100644 --- a/doc/docs/download.md +++ b/doc/docs/download.md @@ -6,14 +6,11 @@ ## Current Version -- [TaxonKit v0.14.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0) -[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0) - - `taxonkit create-taxdump`: - - save taxIds in `int32` instead of `uint32`, as BLAST and DIAMOND do. [#70](https://github.com/shenwei356/taxonkit/issues/70) - - `taxonkit list`: - - do not skip visited subtrees when some of give taxids are descendants of others. [#68](https://github.com/shenwei356/taxonkit/issues/68) - - `taxonkit`: - - when environment variable `TAXONKIT_DB` is set, explicitly setting `--data-dir` will override the value of `TAXONKIT_DB`. +- [TaxonKit v0.14.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.1) +[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/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`. ### Please cite @@ -30,11 +27,11 @@ OS |Arch |File, 中国镜像 |Download Count :------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -Linux |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_linux_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_amd64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_linux_amd64.tar.gz) -Linux |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_linux_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_arm64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_linux_arm64.tar.gz) -macOS |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_darwin_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_amd64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_darwin_amd64.tar.gz) -macOS |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_darwin_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_arm64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_darwin_arm64.tar.gz) -Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_windows_amd64.exe.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_windows_amd64.exe.tar.gz)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_windows_amd64.exe.tar.gz) +Linux |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_linux_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_amd64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_linux_amd64.tar.gz) +Linux |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_linux_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_arm64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_linux_arm64.tar.gz) +macOS |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_darwin_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_amd64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_amd64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_darwin_amd64.tar.gz) +macOS |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_darwin_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_arm64.tar.gz) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_arm64.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_darwin_arm64.tar.gz) +Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_windows_amd64.exe.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_windows_amd64.exe.tar.gz)|[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_windows_amd64.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_windows_amd64.exe.tar.gz) ## Installation @@ -155,6 +152,14 @@ All-in-one command: ## Release history +- [TaxonKit v0.14.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0) +[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0) + - `taxonkit create-taxdump`: + - save taxIds in `int32` instead of `uint32`, as BLAST and DIAMOND do. [#70](https://github.com/shenwei356/taxonkit/issues/70) + - `taxonkit list`: + - do not skip visited subtrees when some of give taxids are descendants of others. [#68](https://github.com/shenwei356/taxonkit/issues/68) + - `taxonkit`: + - when environment variable `TAXONKIT_DB` is set, explicitly setting `--data-dir` will override the value of `TAXONKIT_DB`. - [TaxonKit v0.13.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0) [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.13.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0) - `taxonkit reformat`: diff --git a/doc/docs/tutorial.md b/doc/docs/tutorial.md index 3aceeaf..ca6a52f 100644 --- a/doc/docs/tutorial.md +++ b/doc/docs/tutorial.md @@ -731,9 +731,9 @@ The idea is to export lineages from both GTDB and NCBI using [taxonkit reformat] -R "superkingdom,phylum,class,order,family,genus,species,strain" \ -O taxdump - # we use --field-accession 1 to output the mapping file between old taxids and new ones. - $ grep 2697049 taxdump/taxid.map # SARS-COV-2 - 2697049 21630522 + # we use --field-accession 1 to output the mapping file between old taxids and new ones. + $ grep 2697049 taxdump/taxid.map # SARS-COV-2 + 2697049 21630522 Some tests: diff --git a/doc/docs/usage.md b/doc/docs/usage.md index 26c8d48..6639d0a 100644 --- a/doc/docs/usage.md +++ b/doc/docs/usage.md @@ -699,23 +699,23 @@ Examples: 1. **When these's no nodes of rank "subspecies" nor "strain", you can switch `-S/--pseudo-strain` to use the node with lowest rank - as subspecies/strain name, if which rank is lower than "species"**. + as subspecies/strain name, if which rank is lower than "species"**. Recommend using v0.14.1 or later versions. $ echo -ne "239935\n83333\n1408252\n2697049\n2605619\n" \ | taxonkit lineage -n -r \ - | taxonkit reformat -f '{t};{S};{T}' --fill-miss-rank --pseudo-strain \ + | taxonkit reformat -f '{t};{S};{T}' --pseudo-strain \ | csvtk -H -t cut -f 1,4,3,5 \ | csvtk -H -t sep -f 4 -s ';' -R \ | csvtk -H -t add-header -n "taxid,rank,name,subspecies/strain,subspecies,strain" \ | csvtk pretty -t - taxid rank name subspecies/strain subspecies strain - ------- ---------- ----------------------------------------------- ------------------------------------------------------ ----------------------------------------------- ----------------------------------------------- - 239935 species Akkermansia muciniphila unclassified Akkermansia muciniphila subspecies/strain unclassified Akkermansia muciniphila subspecies unclassified Akkermansia muciniphila strain - 83333 strain Escherichia coli K-12 Escherichia coli K-12 unclassified Escherichia coli subspecies Escherichia coli K-12 - 1408252 subspecies Escherichia coli R178 Escherichia coli R178 Escherichia coli R178 unclassified Escherichia coli R178 strain - 2697049 no rank Severe acute respiratory syndrome coronavirus 2 Severe acute respiratory syndrome coronavirus 2 Severe acute respiratory syndrome coronavirus 2 Severe acute respiratory syndrome coronavirus 2 - 2605619 no rank Escherichia coli O16:H48 Escherichia coli O16:H48 Escherichia coli O16:H48 Escherichia coli O16:H48 + taxid rank name subspecies/strain subspecies strain + ------- ---------- ----------------------------------------------- ----------------------------------------------- ----------------------------------------------- ----------------------------------------------- + 239935 species Akkermansia muciniphila + 83333 strain Escherichia coli K-12 Escherichia coli K-12 Escherichia coli K-12 + 1408252 subspecies Escherichia coli R178 Escherichia coli R178 Escherichia coli R178 + 2697049 no rank Severe acute respiratory syndrome coronavirus 2 Severe acute respiratory syndrome coronavirus 2 Severe acute respiratory syndrome coronavirus 2 Severe acute respiratory syndrome coronavirus 2 + 2605619 no rank Escherichia coli O16:H48 Escherichia coli O16:H48 Escherichia coli O16:H48 Escherichia coli O16:H48 1. Add prefix (`-P/--add-prefix`). @@ -836,7 +836,17 @@ Examples: $ echo -ne "2\n239934\n239935\n" \ | taxonkit lineage \ - | taxonkit reformat -T \ + | taxonkit reformat -F \ + | sed -r "s/;+$//" \ + | csvtk -H -t cut -f 1,3 + + 2 Bacteria;unclassified Bacteria phylum;unclassified Bacteria class;unclassified Bacteria order;unclassified Bacteria family;unclassified Bacteria genus;unclassified Bacteria species + 239934 Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;unclassified Akkermansia species + 239935 Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila + + $ echo -ne "2\n239934\n239935\n" \ + | taxonkit lineage \ + | taxonkit reformat -F -T \ | sed -r "s/;+$//" \ | csvtk -H -t cut -f 1,3