diff --git a/README.md b/README.md index 2aba148..ef89244 100644 --- a/README.md +++ b/README.md @@ -18,9 +18,9 @@ ## Subcommands - `list` list taxon tree of given taxids -- `lineage` query lineage of given taxids from file/stdin -- `reformat` reformat lineage - +- `lineage` query lineage of given taxids (supporting STDIN) +- `reformat` reformat lineage (supporting STDIN) +- `name2taxid` query taxid by taxon scientific name (supporting STDIN) ## Installation @@ -57,7 +57,7 @@ And then: #### Method 3: For Go developer go get -u github.com/shenwei356/taxonkit/taxonkit - + ## Contact Email me for any problem when using taxonkit. shenwei356(at)gmail.com diff --git a/doc/docs/download.md b/doc/docs/download.md index 8b12623..73b66b7 100644 --- a/doc/docs/download.md +++ b/doc/docs/download.md @@ -6,25 +6,23 @@ ## Current Version -[TaxonKit v0.1.8](https://github.com/shenwei356/taxonkit/releases/tag/v0.1.8) -[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.1.8/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.1.8) - -- `taxonkit lineage`, add an extra column of lineage in Taxid. - [#3](https://github.com/shenwei356/taxonkit/issues/3). e.g., +[TaxonKit v0.2.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.0) +[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.2.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.0) - 349741 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;1783257;74201;203494;48461;1647988;239934;239935;349741 -- fix colorful output in windows. +- add command `name2taxid` to query taxid by taxon scientific name. +- `lineage`, `reformat`: ***changed flags and default operations***, + check the [usage](http://bioinf.shenwei.me/taxonkit/usage/). Links: OS |Arch |File, (mirror为中国用户下载镜像链接) |Download Count :------|:---------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- -Linux |32-bit |[taxonkit_linux_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.1.8/taxonkit_linux_386.tar.gz), ([mirror](http://app.shenwei.me/data/taxonkit/taxonkit_linux_386.tar.gz)) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_386.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.1.8/taxonkit_linux_386.tar.gz) -Linux |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.1.8/taxonkit_linux_amd64.tar.gz), ([mirror](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/v0.1.8/taxonkit_linux_amd64.tar.gz) -OS X |32-bit |[taxonkit_darwin_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.1.8/taxonkit_darwin_386.tar.gz), ([mirror](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_386.tar.gz)) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_386.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.1.8/taxonkit_darwin_386.tar.gz) -OS X |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.1.8/taxonkit_darwin_amd64.tar.gz), ([mirror](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/v0.1.8/taxonkit_darwin_amd64.tar.gz) -Windows|32-bit |[taxonkit_windows_386.exe.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.1.8/taxonkit_windows_386.exe.tar.gz), ([mirror](http://app.shenwei.me/data/taxonkit/taxonkit_windows_386.exe.tar.gz)) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_windows_386.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.1.8/taxonkit_windows_386.exe.tar.gz) -Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.1.8/taxonkit_windows_amd64.exe.tar.gz), ([mirror](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/v0.1.8/taxonkit_windows_amd64.exe.tar.gz) +Linux |32-bit |[taxonkit_linux_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.2.0/taxonkit_linux_386.tar.gz), ([mirror](http://app.shenwei.me/data/taxonkit/taxonkit_linux_386.tar.gz)) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_linux_386.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.2.0/taxonkit_linux_386.tar.gz) +Linux |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.2.0/taxonkit_linux_amd64.tar.gz), ([mirror](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/v0.2.0/taxonkit_linux_amd64.tar.gz) +OS X |32-bit |[taxonkit_darwin_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.2.0/taxonkit_darwin_386.tar.gz), ([mirror](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_386.tar.gz)) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_darwin_386.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.2.0/taxonkit_darwin_386.tar.gz) +OS X |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.2.0/taxonkit_darwin_amd64.tar.gz), ([mirror](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/v0.2.0/taxonkit_darwin_amd64.tar.gz) +Windows|32-bit |[taxonkit_windows_386.exe.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.2.0/taxonkit_windows_386.exe.tar.gz), ([mirror](http://app.shenwei.me/data/taxonkit/taxonkit_windows_386.exe.tar.gz)) |[![Github Releases (by Asset)](https://img.shields.io/github/downloads/shenwei356/taxonkit/latest/taxonkit_windows_386.exe.tar.gz.svg?maxAge=3600)](https://github.com/shenwei356/taxonkit/releases/download/v0.2.0/taxonkit_windows_386.exe.tar.gz) +Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.2.0/taxonkit_windows_amd64.exe.tar.gz), ([mirror](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/v0.2.0/taxonkit_windows_amd64.exe.tar.gz) ## Installation @@ -66,6 +64,11 @@ And then: ## Previous Versions +- [TaxonKit v0.1.8](https://github.com/shenwei356/taxonkit/releases/tag/v0.1.8) +[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.1.8/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.1.8) + - `taxonkit lineage`, add an extra column of lineage in Taxid. + [#3](https://github.com/shenwei356/taxonkit/issues/3). e.g., + - fix colorful output in windows. - [TaxonKit v0.1.7](https://github.com/shenwei356/taxonkit/releases/tag/v0.1.7) [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.1.7/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.1.7) - `taxonkit reformat`: supports reading stdin from output of `taxonkit lineage`, diff --git a/doc/docs/usage.md b/doc/docs/usage.md index 31e7055..2b6fa19 100644 --- a/doc/docs/usage.md +++ b/doc/docs/usage.md @@ -15,7 +15,7 @@ Usage ``` TaxonKit - Cross-platform and Efficient NCBI Taxonomy Toolkit -Version: 0.1.8 +Version: 0.2.0 Author: Wei Shen @@ -34,9 +34,11 @@ Usage: taxonkit [command] Available Commands: - lineage query lineage of given taxids from file + help Help about any command + lineage query lineage of given taxids list list taxon tree of given taxids - reformat reformat lineage from stdin + name2taxid query taxid by taxon scientific name + reformat reformat lineage version print version information and check for update Flags: @@ -60,7 +62,7 @@ Usage: taxonkit list [flags] Flags: - --ids string taxid(s), multiple values should be separated by comma (default "1") + --ids string taxid(s), multiple values should be separated by comma --indent string indent (default " ") --json output in JSON format. you can save the result in file with suffix ".json" and open with modern text editor --show-name output scientific name @@ -204,13 +206,14 @@ Examples Usage ``` -query lineage of given taxids from file/stdin +query lineage of given taxids Usage: taxonkit lineage [flags] Flags: - -f, --formated-rank show formated rank + -t, --show-lineage-taxids show lineage consisting of taxids + -i, --taxid-field int field index of taxid. data should be tab-separated (default 1) ``` @@ -228,7 +231,19 @@ Examples 1327037 10000000 - $ taxonkit lineage taxids.txt + + $ taxonkit lineage -t taxids.txt + 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens + 349741 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 + 239935 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila + 11932 Viruses;Retro-transcribing viruses;Retroviridae;unclassified Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle + 314101 cellular organisms;Bacteria;environmental samples;uncultured murine large bowel bacterium BAC 54B + 1327037 Viruses;dsDNA viruses, no RNA stage;Caudovirales;Siphoviridae;unclassified Siphoviridae;Croceibacter phage P2559Y + 10000000 + + show lineage consisting of taxids: + + $ taxonkit lineage -t taxids.txt 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens 131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;40674;32525;9347;1437010;314146;9443;376913;314293;9526;314295;9604;207598;9605;9606 349741 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;1783257;74201;203494;48461;1647988;239934;239935;349741 239935 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;1783257;74201;203494;48461;1647988;239934;239935 @@ -246,7 +261,7 @@ Examples Usage ``` -reformat lineage from stdin +rreformat lineage Output format can be formated by flag --format, available placeholders: @@ -266,7 +281,7 @@ Flags: -d, --delimiter string field delimiter in input lineage (default ";") -F, --fill-miss-rank estimate and fill missing rank with original lineage information (recommended) -f, --format string output format, placeholders of rank are needed (default "{k};{p};{c};{o};{f};{g};{s}") - -c, --lineage-field int field index of lineage. data from stdin should be tab-separated (default 2) + -i, --lineage-field int field index of lineage. data should be tab-separated (default 2) -r, --miss-rank-repl string replacement string for missing rank, if given "", "unclassified xxx xxx" will used ``` @@ -276,59 +291,122 @@ Examples: Example lineage (produced by: `taxonkit lineage taxids.txt > lineage.txt`) $ cat lineage.txt - 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens 131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;40674;32525;9347;1437010;314146;9443;376913;314293;9526;314295;9604;207598;9605;9606 - 349741 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 131567;2;1783257;74201;203494;48461;1647988;239934;239935;349741 - 239935 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila 131567;2;1783257;74201;203494;48461;1647988;239934;239935 - 11932 Viruses;Retro-transcribing viruses;Retroviridae;unclassified Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle 10239;35268;11632;35276;11749;11932 - 314101 cellular organisms;Bacteria;environmental samples;uncultured murine large bowel bacterium BAC 54B 131567;2;48479;314101 - 1327037 Viruses;dsDNA viruses, no RNA stage;Caudovirales;Siphoviridae;unclassified Siphoviridae;Croceibacter phage P2559Y 10239;35237;28883;10699;196894;1327037 - 10000000 + 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens + 349741 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 + 239935 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila + 11932 Viruses;Retro-transcribing viruses;Retroviridae;unclassified Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle + 314101 cellular organisms;Bacteria;environmental samples;uncultured murine large bowel bacterium BAC 54B + 1327037 Viruses;dsDNA viruses, no RNA stage;Caudovirales;Siphoviridae;unclassified Siphoviridae;Croceibacter phage P2559Y 1. Default output format (`"{k};{p};{c};{o};{f};{g};{s}"`) # reformated lineages are appended to the input data + $ taxonkit reformat --lineage-field 2 lineage.txt $ taxonkit reformat lineage.txt - 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens 131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;40674;32525;9347;1437010;314146;9443;376913;314293;9526;314295;9604;207598;9605;9606 Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;Homo sapiens + 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;Homo sapiens ... - 10000000 ;;;;;; - $ taxonkit reformat lineage.txt | cut -f 4 + $ taxonkit reformat lineage.txt | cut -f 3 Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;Homo sapiens Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Viruses;;;;Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle Bacteria;;;;;;uncultured murine large bowel bacterium BAC 54B - Viruses;;;Caudovirales;Siphoviridae;;Croceibacter phage P2559 - ;;;;;; + Viruses;;;Caudovirales;Siphoviridae;;Croceibacter phage P2559Y 1. Use custom strings for unclassfied ranks - $ taxonkit reformat lineage.txt --miss-rank-repl "__" | cut -f 4 + $ taxonkit reformat lineage.txt --miss-rank-repl "__" | cut -f 3 Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;Homo sapiens Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Viruses;__;__;__;Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle Bacteria;__;__;__;__;__;uncultured murine large bowel bacterium BAC 54B Viruses;__;__;Caudovirales;Siphoviridae;__;Croceibacter phage P2559Y - __;__;__;__;__;__;__ 1. Estimate and fill missing rank with original lineage information (**recommended**, very useful for formating input data for [LEfSe](https://bitbucket.org/biobakery/biobakery/wiki/lefse)) - $ taxonkit reformat lineage.txt --fill-miss-rank | cut -f 4 + $ taxonkit reformat lineage.txt --fill-miss-rank | cut -f 3 Eukaryota;Chordata;Mammalia;Primates;Hominidae;Homo;Homo sapiens Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila Viruses;Retro-transcribing viruses;unclassified Viruses class;unclassified Viruses order;Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle Bacteria;environmental samples;unclassified Bacteria class;unclassified Bacteria order;unclassified Bacteria family;unclassified Bacteria genus;uncultured murine large bowel bacterium BAC 54B Viruses;dsDNA viruses, no RNA stage;unclassified Viruses class;Caudovirales;Siphoviridae;unclassified Siphoviridae;Croceibacter phage P2559Y - unclassified superkingdom;unclassified phylum;unclassified class;unclassified order;unclassified family;unclassified genus;unclassified species 1. from taxid to 7-columns lineage: $ cat taxids.txt | taxonkit lineage | taxonkit reformat +## name2taxid + +Usage + +``` +query taxid by taxon scientific name + +Usage: + taxonkit name2taxid [flags] + +Flags: + -i, --name-field int field index of name. data should be tab-separated (default 1) + --show-rank show rank + +``` + +Examples + +Example data + + $ cat names.txt + Homo sapiens + Akkermansia muciniphila ATCC BAA-835 + Akkermansia muciniphila + Mouse Intracisternal A-particle + Wei Shen + uncultured murine large bowel bacterium BAC 54B + Croceibacter phage P2559Y + +1. default + + # taxonkit name2taxid names.txt + $ cat names.txt | taxonkit name2taxid + Homo sapiens 9606 + Akkermansia muciniphila ATCC BAA-835 349741 + Akkermansia muciniphila 239935 + Mouse Intracisternal A-particle 11932 + Wei Shen + uncultured murine large bowel bacterium BAC 54B 314101 + Croceibacter phage P2559Y 1327037 + +1. show rank + + $ cat names.txt | taxonkit name2taxid --show-rank + Homo sapiens 9606 + Akkermansia muciniphila ATCC BAA-835 349741 + Akkermansia muciniphila 239935 + Mouse Intracisternal A-particle 11932 + Wei Shen + uncultured murine large bowel bacterium BAC 54B 314101 + Croceibacter phage P2559Y 1327037 + +1. from name to lineage + + $ cat names.txt | taxonkit name2taxid | taxonkit lineage --taxid-field 2 + Homo sapiens 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens + Akkermansia muciniphila ATCC BAA-835 349741 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila;Akkermansia muciniphila ATCC BAA-835 + Akkermansia muciniphila 239935 cellular organisms;Bacteria;PVC group;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila + Mouse Intracisternal A-particle 11932 Viruses;Retro-transcribing viruses;Retroviridae;unclassified Retroviridae;Intracisternal A-particles;Mouse Intracisternal A-particle + Wei Shen + uncultured murine large bowel bacterium BAC 54B 314101 cellular organisms;Bacteria;environmental samples;uncultured murine large bowel bacterium BAC 54B + Croceibacter phage P2559Y 1327037 Viruses;dsDNA viruses, no RNA stage;Caudovirales;Siphoviridae;unclassified Siphoviridae;Croceibacter phage P2559Y + + $ cat names.txt | taxonkit name2taxid | taxonkit lineage --taxid-field 2 --show-lineage-taxids + Homo sapiens 9606 cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Deuterostomia;Chordata;Craniata;Vertebrata;Gnathostomata;Teleostomi;Euteleostomi;Sarcopterygii;Dipnotetrapodomorpha;Tetrapoda;Amniota;Mammalia;Theria;Eutheria;Boreoeutheria;Euarchontoglires;Primates;Haplorrhini;Simiiformes;Catarrhini;Hominoidea;Hominidae;Homininae;Homo;Homo sapiens 131567;2759;33154;33208;6072;33213;33511;7711;89593;7742;7776;117570;117571;8287;1338369;32523;32524;40674;32525;9347;1437010;314146;9443;376913;314293;9526;314295;9604;207598;9605;9606 + ... +