diff --git a/README.md b/README.md index ef89244..2626327 100644 --- a/README.md +++ b/README.md @@ -22,6 +22,11 @@ - `reformat` reformat lineage (supporting STDIN) - `name2taxid` query taxid by taxon scientific name (supporting STDIN) +Misc + +- `version` print version information and check for update +- `genautocomplete` generate shell autocompletion script + ## Installation Go to [Download Page](http://bioinf.shenwei.me/taxonkit/download) for more download options and changelogs. @@ -58,6 +63,25 @@ And then: go get -u github.com/shenwei356/taxonkit/taxonkit +## Bash-completion + +Note: The current version supports Bash only. +This should work for *nix systems with Bash installed. + +Howto: + +1. run: `taxonkit genautocomplete` + +2. create and edit `~/.bash_completion` file if you don't have it. + + nano ~/.bash_completion + + add the following: + + for bcfile in ~/.bash_completion.d/* ; do + . $bcfile + done + ## 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 19c9525..bde6933 100644 --- a/doc/docs/download.md +++ b/doc/docs/download.md @@ -6,23 +6,25 @@ ## Current Version -[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) +[TaxonKit v0.2.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.1) +[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.2.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.1) -- 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/). +- `taxonkit list`: fix bug of no output for leaf nodes of the taxonomic tree. +[#4](https://github.com/shenwei356/taxonkit/issues/4) +- add new command `genautocomplete` to generate **shell autocompletion** script! Links: +***Tip: run `taxonkit version` to check update !!!*** + 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/v0.2.0/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) +Linux |32-bit |[taxonkit_linux_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.2.1/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/v0.2.1/taxonkit_linux_386.tar.gz) +Linux |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.2.1/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/v0.2.1/taxonkit_linux_amd64.tar.gz) +OS X |32-bit |[taxonkit_darwin_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.2.1/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/v0.2.1/taxonkit_darwin_386.tar.gz) +OS X |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.2.1/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/v0.2.1/taxonkit_darwin_amd64.tar.gz) +Windows|32-bit |[taxonkit_windows_386.exe.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.2.1/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/v0.2.1/taxonkit_windows_386.exe.tar.gz) +Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.2.1/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/v0.2.1/taxonkit_windows_amd64.exe.tar.gz) ## Installation @@ -61,9 +63,32 @@ And then: go get -u github.com/shenwei356/taxonkit/taxonkit +## Bash-completion + +Note: The current version supports Bash only. +This should work for *nix systems with Bash installed. + +Howto: + +1. run: `taxonkit genautocomplete` + +2. create and edit `~/.bash_completion` file if you don't have it. + + nano ~/.bash_completion + + add the following: + + for bcfile in ~/.bash_completion.d/* ; do + . $bcfile + done ## Previous Versions +- [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) + - 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/). - [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. diff --git a/doc/docs/usage.md b/doc/docs/usage.md index d59a4e7..8a7e5bb 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: 0.2.0 +Version: 0.2.1 Author: Wei Shen @@ -34,14 +34,16 @@ Usage: taxonkit [command] Available Commands: - help Help about any command - lineage query lineage of given taxids - list list taxon tree of given taxids - name2taxid query taxid by taxon scientific name - reformat reformat lineage - version print version information and check for update + genautocomplete generate shell autocompletion script + help Help about any command + lineage query lineage of given taxids + list list taxon tree of given taxids + name2taxid query taxid by taxon scientific name + reformat reformat lineage + version print version information and check for update Flags: + -h, --help help for taxonkit --names-file string names.dmp file (default "/home/shenwei/.taxonkit/names.dmp") --nodes-file string nodes.dmp file (default "/home/shenwei/.taxonkit/nodes.dmp") -o, --out-file string out file ("-" for stdout, suffix .gz for gzipped out) (default "-") @@ -407,6 +409,39 @@ Example data 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 ... +## genautocomplete + +Usage + +``` +generate shell autocompletion script + +Note: The current version supports Bash only. +This should work for *nix systems with Bash installed. + +Howto: + +1. run: taxonkit genautocomplete + +2. create and edit ~/.bash_completion file if you don't have it. + + nano ~/.bash_completion + + add the following: + + for bcfile in ~/.bash_completion.d/* ; do + . $bcfile + done + +Usage: + taxonkit genautocomplete [flags] + +Flags: + --file string autocompletion file (default "/home/shenwei/.bash_completion.d/taxonkit.sh") + -h, --help help for genautocomplete + --type string autocompletion type (currently only bash supported) (default "bash") + +```