v0.14.1

shenwei356 · Dec 21, 2022 · dc61908 · dc61908
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diff --git a/doc/docs/download.md b/doc/docs/download.md
@@ -6,14 +6,11 @@
 
 ## Current Version
 
-- [TaxonKit v0.14.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0)
-    - `taxonkit create-taxdump`:
-        - save taxIds in `int32` instead of `uint32`, as BLAST and DIAMOND do. [#70](https://github.com/shenwei356/taxonkit/issues/70)
-    - `taxonkit list`:
-        - do not skip visited subtrees when some of give taxids are descendants of others. [#68](https://github.com/shenwei356/taxonkit/issues/68)
-    - `taxonkit`:
-        - when environment variable `TAXONKIT_DB` is set, explicitly setting `--data-dir` will override the value of `TAXONKIT_DB`.
+- [TaxonKit v0.14.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.1)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.1)
+    - `taxonkit reformat`:
+        - The flag `-S/--pseudo-strain` does not require `-F/--fill-miss-rank` now.
+        - For taxa of rank >= species, `{t}`, `{S}`, and `T` outputs nothing when using `-S/--pseudo-strain`.
 
 ### Please cite
 
@@ -30,11 +27,11 @@
 
 OS     |Arch      |File, 中国镜像                                                                                                                                                                              |Download Count
 :------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/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/v0.14.0/taxonkit_linux_amd64.tar.gz)
-Linux  |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_linux_arm64.tar.gz),<br/> [中国镜像](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/v0.14.0/taxonkit_linux_arm64.tar.gz)
-macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/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/v0.14.0/taxonkit_darwin_amd64.tar.gz)
-macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/taxonkit_darwin_arm64.tar.gz),<br/> [中国镜像](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/v0.14.0/taxonkit_darwin_arm64.tar.gz)
-Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.0/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/v0.14.0/taxonkit_windows_amd64.exe.tar.gz)
+Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/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/v0.14.1/taxonkit_linux_amd64.tar.gz)
+Linux  |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_linux_arm64.tar.gz),<br/> [中国镜像](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/v0.14.1/taxonkit_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/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/v0.14.1/taxonkit_darwin_amd64.tar.gz)
+macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/taxonkit_darwin_arm64.tar.gz),<br/> [中国镜像](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/v0.14.1/taxonkit_darwin_arm64.tar.gz)
+Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.14.1/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/v0.14.1/taxonkit_windows_amd64.exe.tar.gz)
 
 ## Installation
 
@@ -155,6 +152,14 @@ All-in-one command:
 
 ## Release history
 
+- [TaxonKit v0.14.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.0)
+    - `taxonkit create-taxdump`:
+        - save taxIds in `int32` instead of `uint32`, as BLAST and DIAMOND do. [#70](https://github.com/shenwei356/taxonkit/issues/70)
+    - `taxonkit list`:
+        - do not skip visited subtrees when some of give taxids are descendants of others. [#68](https://github.com/shenwei356/taxonkit/issues/68)
+    - `taxonkit`:
+        - when environment variable `TAXONKIT_DB` is set, explicitly setting `--data-dir` will override the value of `TAXONKIT_DB`.
 - [TaxonKit v0.13.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.13.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.13.0)
     - `taxonkit reformat`:

diff --git a/doc/docs/tutorial.md b/doc/docs/tutorial.md
@@ -731,9 +731,9 @@ The idea is to export lineages from both GTDB and NCBI using [taxonkit reformat]
                 -R "superkingdom,phylum,class,order,family,genus,species,strain" \
                 -O taxdump
 
-       # we use --field-accession  1 to output the mapping file between old taxids and new ones.
-       $ grep 2697049  taxdump/taxid.map  # SARS-COV-2
-       2697049 21630522
+        # we use --field-accession  1 to output the mapping file between old taxids and new ones.
+        $ grep 2697049  taxdump/taxid.map  # SARS-COV-2
+        2697049 21630522
 
 Some tests:
 

diff --git a/doc/docs/usage.md b/doc/docs/usage.md
@@ -699,23 +699,23 @@ Examples:
 
 1. **When these's no nodes of rank "subspecies" nor "strain",
    you 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"**. Recommend using v0.14.1 or later versions.
 
         $ echo -ne "239935\n83333\n1408252\n2697049\n2605619\n" \
             | taxonkit lineage -n -r \
-            | taxonkit reformat -f '{t};{S};{T}' --fill-miss-rank  --pseudo-strain \
+            | taxonkit reformat -f '{t};{S};{T}' --pseudo-strain \
             | csvtk -H -t cut -f 1,4,3,5 \
             | csvtk -H -t sep -f 4 -s ';' -R \
             | csvtk -H -t add-header -n "taxid,rank,name,subspecies/strain,subspecies,strain" \
             | csvtk pretty -t
             
-        taxid     rank         name                                              subspecies/strain                                        subspecies                                        strain
-        -------   ----------   -----------------------------------------------   ------------------------------------------------------   -----------------------------------------------   -----------------------------------------------
-        239935    species      Akkermansia muciniphila                           unclassified Akkermansia muciniphila subspecies/strain   unclassified Akkermansia muciniphila subspecies   unclassified Akkermansia muciniphila strain
-        83333     strain       Escherichia coli K-12                             Escherichia coli K-12                                    unclassified Escherichia coli subspecies          Escherichia coli K-12
-        1408252   subspecies   Escherichia coli R178                             Escherichia coli R178                                    Escherichia coli R178                             unclassified Escherichia coli R178 strain
-        2697049   no rank      Severe acute respiratory syndrome coronavirus 2   Severe acute respiratory syndrome coronavirus 2          Severe acute respiratory syndrome coronavirus 2   Severe acute respiratory syndrome coronavirus 2
-        2605619   no rank      Escherichia coli O16:H48                          Escherichia coli O16:H48                                 Escherichia coli O16:H48                          Escherichia coli O16:H48
+        taxid     rank         name                                              subspecies/strain                                 subspecies                                        strain
+        -------   ----------   -----------------------------------------------   -----------------------------------------------   -----------------------------------------------   -----------------------------------------------
+        239935    species      Akkermansia muciniphila
+        83333     strain       Escherichia coli K-12                             Escherichia coli K-12                                                                               Escherichia coli K-12
+        1408252   subspecies   Escherichia coli R178                             Escherichia coli R178                             Escherichia coli R178
+        2697049   no rank      Severe acute respiratory syndrome coronavirus 2   Severe acute respiratory syndrome coronavirus 2   Severe acute respiratory syndrome coronavirus 2   Severe acute respiratory syndrome coronavirus 2
+        2605619   no rank      Escherichia coli O16:H48                          Escherichia coli O16:H48                          Escherichia coli O16:H48                          Escherichia coli O16:H48
 
 1. Add prefix (`-P/--add-prefix`).
 
@@ -836,7 +836,17 @@ Examples:
 
         $ echo -ne "2\n239934\n239935\n" \
             | taxonkit lineage \
-            | taxonkit reformat -T \
+            | taxonkit reformat -F \
+            | sed -r "s/;+$//" \
+            | csvtk -H -t cut -f 1,3
+
+        2       Bacteria;unclassified Bacteria phylum;unclassified Bacteria class;unclassified Bacteria order;unclassified Bacteria family;unclassified Bacteria genus;unclassified Bacteria species
+        239934  Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;unclassified Akkermansia species
+        239935  Bacteria;Verrucomicrobia;Verrucomicrobiae;Verrucomicrobiales;Akkermansiaceae;Akkermansia;Akkermansia muciniphila
+
+        $ echo -ne "2\n239934\n239935\n" \
+            | taxonkit lineage \
+            | taxonkit reformat -F -T \
             | sed -r "s/;+$//" \
             | csvtk -H -t cut -f 1,3