v0.6.1

shenwei356 · Oct 30, 2020 · bbd0bae · bbd0bae
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diff --git a/doc/docs/download.md b/doc/docs/download.md
@@ -6,13 +6,15 @@
 
 ## Current Version
 
-- [TaxonKit v0.6.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.6.0)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.6.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.6.0)
-    - `taxonkit list`:
-        - check merged and deleted taxids.
-        - fix bug of json output. [#30](https://github.com/shenwei356/taxonkit/issues/30)
-    - `taxonkit name2taxid`: new flag `-s/--sci-name` for limiting to searching scientific names. [#29](https://github.com/shenwei356/taxonkit/issues/29)
-    - `taxonkit version`: make checking update optional
+- [TaxonKit v0.6.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.6.1)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.6.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.6.1)
+    - `taxonkit lineage`: 
+        - new flag `-n/--show-name` for appending scientific name.
+        - new flag `-L/--no-lineage` for hide lineage, this is for fast retrieving names or/and ranks.
+    - `taxonkit reformat`:
+        - fix flag `-F/--fill-miss-rank`.
+        - discard order restriction of rank symbols.
+
 
 Links:
 
@@ -24,12 +26,12 @@ 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/v0.6.0/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/v0.6.0/taxonkit_linux_386.tar.gz)
-Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.6.0/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/v0.6.0/taxonkit_linux_amd64.tar.gz)
-OS X   |32-bit    |[taxonkit_darwin_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.6.0/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/v0.6.0/taxonkit_darwin_386.tar.gz)
-OS X   |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.6.0/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/v0.6.0/taxonkit_darwin_amd64.tar.gz)
-Windows|32-bit    |[taxonkit_windows_386.exe.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.6.0/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/v0.6.0/taxonkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.6.0/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/v0.6.0/taxonkit_windows_amd64.exe.tar.gz)
+Linux  |32-bit    |[taxonkit_linux_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.6.1/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/v0.6.1/taxonkit_linux_386.tar.gz)
+Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.6.1/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/v0.6.1/taxonkit_linux_amd64.tar.gz)
+OS X   |32-bit    |[taxonkit_darwin_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.6.1/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/v0.6.1/taxonkit_darwin_386.tar.gz)
+OS X   |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.6.1/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/v0.6.1/taxonkit_darwin_amd64.tar.gz)
+Windows|32-bit    |[taxonkit_windows_386.exe.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.6.1/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/v0.6.1/taxonkit_windows_386.exe.tar.gz)
+Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.6.1/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/v0.6.1/taxonkit_windows_amd64.exe.tar.gz)
 
 
 ## Installation
@@ -91,6 +93,13 @@ Howto:
 
 ## Previous Versions
 
+- [TaxonKit v0.6.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.6.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.6.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.6.0)
+    - `taxonkit list`:
+        - check merged and deleted taxids.
+        - fix bug of json output. [#30](https://github.com/shenwei356/taxonkit/issues/30)
+    - `taxonkit name2taxid`: new flag `-s/--sci-name` for limiting to searching scientific names. [#29](https://github.com/shenwei356/taxonkit/issues/29)
+    - `taxonkit version`: make checking update optional
 - [TaxonKit v0.5.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.5.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.5.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.5.0)
     - `taxonkit`: requiring delnodes.dmp and merged.dmp.

diff --git a/doc/docs/tutorial.md b/doc/docs/tutorial.md
@@ -47,6 +47,7 @@ Steps:
         # 6656    cellular organisms;Eukaryota;Opisthokonta;Metazoa;Eumetazoa;Bilateria;Protostomia;Ecdysozoa;Panarthropoda;Arthropoda    Eukaryota;Arthropoda;;;;;
         
         # 2    bacteria
+        # 2157 archaea
         # 4751 fungi
         # 10239 virus
 

diff --git a/doc/docs/usage.md b/doc/docs/usage.md
@@ -27,7 +27,7 @@ And copy "names.dmp", "nodes.dmp", "delnodes.dmp" and "merged.dmp" to data direc
 ```text
 TaxonKit - A Cross-platform and Efficient NCBI Taxonomy Toolkit
 
-Version: 0.6.0
+Version: 0.6.1
 
 Author: Wei Shen <shenwei356@gmail.com>
 
@@ -276,7 +276,9 @@ Usage:
 Flags:
   -d, --delimiter string      field delimiter in lineage (default ";")
   -h, --help                  help for lineage
+  -L, --no-lineage            do not show lineage, when user just want names or/and ranks
   -t, --show-lineage-taxids   appending lineage consisting of taxids
+  -n, --show-name             appending scientific name
   -r, --show-rank             appending rank of taxids
   -c, --show-status-code      show status code between lineage
   -i, --taxid-field int       field index of taxid. data should be tab-separated (default 1)
@@ -365,24 +367,22 @@ Examples
             | csvtk filter2 -H -t -f '$5>0' \
             | csvtk -H -t cut -f -3
 
-1. Show rank
-
-        $ taxonkit lineage -r taxids.txt | cut -f 1,3 | csvtk pretty -t
-        9606        species
-        9913        species
-        376619      strain
-        349741      strain
-        239935      species
-        314101      species
-        11932       species
-        1327037     species
-        123124124   
-        3           
-        92489       species
-        1458427     species
-
-
-        
+1. Only show name and rank
+
+        $ taxonkit lineage -r -n -L taxids.txt | csvtk pretty -t
+        9606        Homo sapiens                                      species
+        9913        Bos taurus                                        species
+        376619      Francisella tularensis subsp. holarctica LVS      strain
+        349741      Akkermansia muciniphila ATCC BAA-835              strain
+        239935      Akkermansia muciniphila                           species
+        314101      uncultured murine large bowel bacterium BAC 54B   species
+        11932       Mouse Intracisternal A-particle                   species
+        1327037     Croceibacter phage P2559Y                         species
+        123124124                                                     
+        3                                                             
+        92489       Erwinia oleae                                     species
+        1458427     Serpentinomonas raichei                           species
+
 
 1. Show lineage consisting of taxids: