v0.3.0

HISTORY.md

@@ -1,3 +1,6 @@
+- [TaxonKit v0.3.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.3.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.3.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.3.0)
+    - this version is almost the same as v0.2.5
 - [TaxonKit v0.2.5](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.5)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.2.5/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.5)
     - add global flag: `--line-buffered` to disable output buffer. [#11](https://github.com/shenwei356/taxonkit/issues/11)

README.md

@@ -1,4 +1,4 @@
-# TaxonKit - Cross-platform and Efficient NCBI Taxonomy Toolkit
+# TaxonKit - A cross-platform and Efficient NCBI Taxonomy Toolkit
 
 - **Documents:** [http://bioinf.shenwei.me/taxonkit](http://bioinf.shenwei.me/taxonkit)
 ([**Usage**](http://bioinf.shenwei.me/taxonkit/usage/),

doc/docs/download.md

@@ -6,13 +6,9 @@
 
 ## Current Version
 
-- [TaxonKit v0.2.5](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.5)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.2.5/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.5)
-    - add global flag: `--line-buffered` to disable output buffer. [#11](https://github.com/shenwei356/taxonkit/issues/11)
-    - replace global flags `--names-file` and `--nodes-file` with `--data-dir`, also support environment variable `TAXONKIT_DB`. [#17](https://github.com/shenwei356/taxonkit/issues/17)
-    - `taxonkit reformat`: detects lineages containing unofficial taxon name and won't show panic message.
-    - `taxonkit name2taxid`: supports synonyms names. [#9](https://github.com/shenwei356/taxonkit/commit/d4fac1c1138a571957f52eb431ff0d85c03852a8)
-    - `taxokit lineage`: add flag `-r/--show-rank` to print rank at another new column.
+- [TaxonKit v0.3.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.3.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.3.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.3.0)
+    - this version is almost the same as v0.2.5
 
 Links:
 
@@ -24,12 +20,12 @@ Links:
 
 OS     |Arch      |File, 中国镜像                                                                                                                                                                              |Download Count
 :------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |32-bit    |[taxonkit_linux_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.2.5/taxonkit_linux_386.tar.gz),<br/> [中国镜像](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/v0.2.5/taxonkit_linux_386.tar.gz)
-Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.2.5/taxonkit_linux_amd64.tar.gz),<br/> [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/v0.2.5/taxonkit_linux_amd64.tar.gz)
-OS X   |32-bit    |[taxonkit_darwin_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.2.5/taxonkit_darwin_386.tar.gz),<br/> [中国镜像](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/v0.2.5/taxonkit_darwin_386.tar.gz)
-OS X   |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.2.5/taxonkit_darwin_amd64.tar.gz),<br/> [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/v0.2.5/taxonkit_darwin_amd64.tar.gz)
-Windows|32-bit    |[taxonkit_windows_386.exe.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.2.5/taxonkit_windows_386.exe.tar.gz),<br/> [中国镜像](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/v0.2.5/taxonkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.2.5/taxonkit_windows_amd64.exe.tar.gz),<br/> [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/v0.2.5/taxonkit_windows_amd64.exe.tar.gz)
+Linux  |32-bit    |[taxonkit_linux_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.3.0/taxonkit_linux_386.tar.gz),<br/> [中国镜像](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/v0.3.0/taxonkit_linux_386.tar.gz)
+Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.3.0/taxonkit_linux_amd64.tar.gz),<br/> [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/v0.3.0/taxonkit_linux_amd64.tar.gz)
+OS X   |32-bit    |[taxonkit_darwin_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.3.0/taxonkit_darwin_386.tar.gz),<br/> [中国镜像](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/v0.3.0/taxonkit_darwin_386.tar.gz)
+OS X   |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.3.0/taxonkit_darwin_amd64.tar.gz),<br/> [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/v0.3.0/taxonkit_darwin_amd64.tar.gz)
+Windows|32-bit    |[taxonkit_windows_386.exe.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.3.0/taxonkit_windows_386.exe.tar.gz),<br/> [中国镜像](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/v0.3.0/taxonkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.3.0/taxonkit_windows_amd64.exe.tar.gz),<br/> [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/v0.3.0/taxonkit_windows_amd64.exe.tar.gz)
 
 
 ## Installation
@@ -91,6 +87,13 @@ Howto:
 
 ## Previous Versions
 
+- [TaxonKit v0.2.5](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.5)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.2.5/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.5)
+    - add global flag: `--line-buffered` to disable output buffer. [#11](https://github.com/shenwei356/taxonkit/issues/11)
+    - replace global flags `--names-file` and `--nodes-file` with `--data-dir`, also support environment variable `TAXONKIT_DB`. [#17](https://github.com/shenwei356/taxonkit/issues/17)
+    - `taxonkit reformat`: detects lineages containing unofficial taxon name and won't show panic message.
+    - `taxonkit name2taxid`: supports synonyms names. [#9](https://github.com/shenwei356/taxonkit/commit/d4fac1c1138a571957f52eb431ff0d85c03852a8)
+    - `taxokit lineage`: add flag `-r/--show-rank` to print rank at another new column.
 - [TaxonKit v0.2.4](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.4)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.2.4/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.2.4)
     - `taxonkit reformat`:

doc/docs/usage.md

@@ -11,9 +11,9 @@ And copy "names.dmp" and "nodes.dmp" to data directory: "$HOME/.taxonkit".
 ## taxonkit
 
 ```
-TaxonKit - Cross-platform and Efficient NCBI Taxonomy Toolkit
+TaxonKit - A cross-platform and Efficient NCBI Taxonomy Toolkit
 
-Version: 0.2.5
+Version: 0.3.0
 
 Author: Wei Shen <[email protected]>
 
@@ -217,6 +217,7 @@ Flags:
   -d, --delimiter string      field delimiter in lineage (default ";")
   -h, --help                  help for lineage
   -t, --show-lineage-taxids   show lineage consisting of taxids
+  -r, --show-rank             show rank of taxids
   -i, --taxid-field int       field index of taxid. data should be tab-separated (default 1)
 
 ```
@@ -244,7 +245,7 @@ Examples
         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
-        
+
 1. Show rank
 
         $ taxonkit lineage -r taxids.txt | cut -f 1,3

taxonkit/cmd/helper.go

@@ -34,7 +34,7 @@ import (
 )
 
 // VERSION of csvtk
-const VERSION = "0.2.5"
+const VERSION = "0.3.0"
 
 // Config is the struct containing all global flags
 type Config struct {
@@ -61,8 +61,7 @@ func getConfigs(cmd *cobra.Command) Config {
 		log.Errorf(`data directory not created. please download and decompress ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz, and copy "names.dmp" and "nodes.dmp" to %s`, dataDir)
 	}
 
-	return Config{
-		Threads:      getFlagPositiveInt(cmd, "threads"),
+	return Config{Threads: getFlagPositiveInt(cmd, "threads"),
 		OutFile:      getFlagString(cmd, "out-file"),
 		DataDir:      dataDir,
 		NodesFile:    filepath.Join(dataDir, "nodes.dmp"),

taxonkit/cmd/root.go

@@ -54,7 +54,7 @@ func init() {
 	defaulDataDir, err = homedir.Expand("~/.taxonkit/")
 	checkError(errors.Wrap(err, "get data directory"))
 
-	RootCmd.Long = fmt.Sprintf(`TaxonKit - Cross-platform and Efficient NCBI Taxonomy Toolkit
+	RootCmd.Long = fmt.Sprintf(`TaxonKit - A cross-platform and Efficient NCBI Taxonomy Toolkit
 
 Version: %s