update doc

shenwei356 · Jan 26, 2021 · 98a37c4 · 98a37c4
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diff --git a/doc/docs/download.md b/doc/docs/download.md
@@ -6,12 +6,17 @@
 
 ## Current Version
 
-- [TaxonKit v0.7.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.7.1)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.7.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.7.1)
-    - `taxonkit filter`: 
-        - disable unnecessary stdin check when using flag `--list-order` or `--list-ranks`. [#36](https://github.com/shenwei356/taxonkit/issues/36)
-        - better handling of black list, empty default value: "no rank" and "clade". And you need use `-N/--discard-noranks` to explicitly filter out "no rank", "clade". [#37](https://github.com/shenwei356/taxonkit/issues/37)
-        - update help message. Thanks @standage for improve this command! [#38](https://github.com/shenwei356/taxonkit/issues/38)
+- [TaxonKit v0.7.2](https://github.com/shenwei356/taxonkit/releases/tag/v0.7.2)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.7.2/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.7.2)
+    - `taxonkit lineage`:
+        - new flag `-R/--show-lineage-ranks` for appending ranks of all levels.
+        - reduce memory occupation and slightly speedup.
+    - `taxonkit filter`:
+        - flag `-E/--equal-to` supports multiple values.
+        - new flag `-n/--save-predictable-norank`: do not discard some special ranks without order when using -L, where rank of the closest higher node is still lower than rank cutoff.
+    - `taxonkit reformat`:
+        - **new placeholder `{t}` for `subspecies/strain`, `{T}` for `strain`**. Thanks @wqssf102 for feedback.
+        - new flag `-S/--pseudo-strain` for using the node with lowest rank as strain name, only if which rank is lower than "species" and not "subpecies" nor "strain". 
 
 Links:
 
@@ -23,11 +28,11 @@ Links:
 
 OS     |Arch      |File, 备用镜像                                                                                                                                                                              |Download Count
 :------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.1/taxonkit_linux_amd64.tar.gz),<br/> [备用镜像](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/v0.7.1/taxonkit_linux_amd64.tar.gz)
-Linux  |**arm64**|[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.1/taxonkit_linux_arm64.tar.gz),<br/> [备用镜像](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/v0.7.1/taxonkit_linux_arm64.tar.gz)
-macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.1/taxonkit_darwin_amd64.tar.gz),<br/> [备用镜像](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/v0.7.1/taxonkit_darwin_amd64.tar.gz)
-macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.1/taxonkit_darwin_arm64.tar.gz),<br/> [备用镜像](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/v0.7.1/taxonkit_darwin_arm64.tar.gz)
-Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.1/taxonkit_windows_amd64.exe.tar.gz),<br/> [备用镜像](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/v0.7.1/taxonkit_windows_amd64.exe.tar.gz)
+Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.2/taxonkit_linux_amd64.tar.gz),<br/> [备用镜像](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/v0.7.2/taxonkit_linux_amd64.tar.gz)
+Linux  |**arm64**|[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.2/taxonkit_linux_arm64.tar.gz),<br/> [备用镜像](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/v0.7.2/taxonkit_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.2/taxonkit_darwin_amd64.tar.gz),<br/> [备用镜像](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/v0.7.2/taxonkit_darwin_amd64.tar.gz)
+macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.2/taxonkit_darwin_arm64.tar.gz),<br/> [备用镜像](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/v0.7.2/taxonkit_darwin_arm64.tar.gz)
+Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.2/taxonkit_windows_amd64.exe.tar.gz),<br/> [备用镜像](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/v0.7.2/taxonkit_windows_amd64.exe.tar.gz)
 
 
 ## Installation
@@ -105,6 +110,13 @@ All-in-one command:
 
 ## Previous Versions
 
+        
+- [TaxonKit v0.7.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.7.1)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.7.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.7.1)
+    - `taxonkit filter`: 
+        - disable unnecessary stdin check when using flag `--list-order` or `--list-ranks`. [#36](https://github.com/shenwei356/taxonkit/issues/36)
+        - better handling of black list, empty default value: "no rank" and "clade". And you need use `-N/--discard-noranks` to explicitly filter out "no rank", "clade". [#37](https://github.com/shenwei356/taxonkit/issues/37)
+        - update help message. Thanks @standage for improve this command! [#38](https://github.com/shenwei356/taxonkit/issues/38)
 - [TaxonKit v0.7.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.7.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.7.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.7.0)
     - `taxonkit`: **2-3X faster taxonomy data loading**.

diff --git a/doc/docs/tutorial.md b/doc/docs/tutorial.md
@@ -126,9 +126,9 @@ Fill missing ranks and add prefixes.
     2605619   k__Bacteria   p__Proteobacteria                 c__Gammaproteobacteria           o__Enterobacterales              f__Enterobacteriaceae             g__Escherichia                       s__Escherichia coli                                        t__unclassified Escherichia coli subspecies/strain
     2697049   k__Viruses    p__Pisuviricota                   c__Pisoniviricetes               o__Nidovirales                   f__Coronaviridae                  g__Betacoronavirus                   s__Severe acute respiratory syndrome-related coronavirus   t__unclassified Severe acute respiratory syndrome-related coronavirus subspecies/strain
 
-When these's no nodes of rank "subspecies" nor "stain",
+**When these's no nodes of rank "subspecies" nor "stain",
 we 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"**.
 
     $ cat taxids3.txt \
         | taxonkit lineage -r \
@@ -150,8 +150,8 @@ as subspecies/strain name, if which rank is lower than "species".
 
 List eight-level lineage for all taxIDs of rank lower than or equal to species, including some nodes with "no rank".
 But when filtering with `-L/--lower-than`, you can use
-`-n/--save-predictable-norank` to save some special ranks without order,
-where rank of the closest higher node is still lower than rank cutoff.
+`-n/--save-predictable-norank` to **save some special ranks without order,
+where rank of the closest higher node is still lower than rank cutoff**.
 
     $ time taxonkit list --ids 1 \
         | taxonkit filter -L species -E species -R -N -n \

diff --git a/doc/docs/usage.md b/doc/docs/usage.md
@@ -360,7 +360,7 @@ Examples
         92489   cellular organisms;Bacteria;Proteobacteria;Gammaproteobacteria;Enterobacterales;Erwiniaceae;Erwinia;Erwinia oleae
         1458427 cellular organisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raicheisms;Bacteria;Proteobacteria;Betaproteobacteria;Burkholderiales;Comamonadaceae;Serpentinomonas;Serpentinomonas raichei
 
-1. Speed
+1. Speed.
 
         $ time echo 9606 | taxonkit lineage 
         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
@@ -406,8 +406,8 @@ Examples
         $ cat lineage.withcode.txt | awk '$2 < 0' | cut -f 1
         123124124
 
-1. **Filter out invalid and deleted taxids, and *replace merged taxids with new ones"**,
-  you may install [csvtk](https://github.com/shenwei356/csvtk.
+1. **Filter out invalid and deleted taxids, and replace merged taxids with new ones**,
+  you may install [csvtk](https://github.com/shenwei356/csvtk).
 
         # input is one-column-taxid
         $ taxonkit lineage -c taxids.txt \