add a new tutorial

shenwei356 · Nov 24, 2023 · 9e5f985 · 9e5f985
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diff --git a/README.md b/README.md
@@ -64,7 +64,7 @@ Subcommand                                                                    |F
 [`list`](https://bioinf.shenwei.me/taxonkit/usage/#list)                      |List taxonomic subtrees (TaxIds) bellow given TaxIds
 [`lineage`](https://bioinf.shenwei.me/taxonkit/usage/#lineage)                |Query taxonomic lineage of given TaxIds
 [`reformat`](https://bioinf.shenwei.me/taxonkit/usage/#reformat)              |Reformat lineage in canonical ranks
-[`name2taxid`](https://bioinf.shenwei.me/taxonkit/usage/#name2taxid)          |Convert scientific names to TaxIds
+[`name2taxid`](https://bioinf.shenwei.me/taxonkit/usage/#name2taxid)          |Convert taxon names to TaxIds
 [`filter`](https://bioinf.shenwei.me/taxonkit/usage/#filter)                  |Filter TaxIds by taxonomic rank range
 [`lca`](https://bioinf.shenwei.me/taxonkit/usage/#lca)                        |Compute lowest common ancestor (LCA) for TaxIds
 [`taxid-changelog`](https://bioinf.shenwei.me/taxonkit/usage/#taxid-changelog)|Create TaxId changelog from dump archives

diff --git a/doc/docs/download.md b/doc/docs/download.md
@@ -6,12 +6,10 @@
 
 ## Current Version
 
-- [TaxonKit v0.15.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.15.0)
-[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.15.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.15.0)
-    - `taxonkit reformat`:
-        - For lineages with more than one node, if it fails to query TaxId with the parent-child pair, use the last child only. [#82](https://github.com/shenwei356/taxonkit/issues/82)
-        - The flag `-T/--trim` also does not add the prefix for missing ranks lower than the current rank. [#82](https://github.com/shenwei356/taxonkit/issues/82)
-        - New flag `-s/--miss-rank-repl-suffix` to set the suffix for estimated taxon names. [#85](https://github.com/shenwei356/taxonkit/issues/85)
+- [TaxonKit v0.15.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.15.1)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.15.1/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.15.1)
+    - `taxonkit name2taxid`:
+        - remove the restriction of name types. [#87](https://github.com/shenwei356/taxonkit/issues/87)
 
 ### Please cite
 
@@ -28,11 +26,11 @@
 
 OS     |Arch      |File, 中国镜像                                                                                                                                                                              |Download Count
 :------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.15.0/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/v0.15.0/taxonkit_linux_amd64.tar.gz)
-Linux  |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.15.0/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/v0.15.0/taxonkit_linux_arm64.tar.gz)
-macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.15.0/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/v0.15.0/taxonkit_darwin_amd64.tar.gz)
-macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.15.0/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/v0.15.0/taxonkit_darwin_arm64.tar.gz)
-Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.15.0/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/v0.15.0/taxonkit_windows_amd64.exe.tar.gz)
+Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.15.1/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/v0.15.1/taxonkit_linux_amd64.tar.gz)
+Linux  |**arm64** |[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.15.1/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/v0.15.1/taxonkit_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.15.1/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/v0.15.1/taxonkit_darwin_amd64.tar.gz)
+macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.15.1/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/v0.15.1/taxonkit_darwin_arm64.tar.gz)
+Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.15.1/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/v0.15.1/taxonkit_windows_amd64.exe.tar.gz)
 
 ## Installation
 
@@ -153,6 +151,12 @@ All-in-one command:
 
 ## Release history
 
+- [TaxonKit v0.15.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.15.0)
+[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.15.0/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.15.0)
+    - `taxonkit reformat`:
+        - For lineages with more than one node, if it fails to query TaxId with the parent-child pair, use the last child only. [#82](https://github.com/shenwei356/taxonkit/issues/82)
+        - The flag `-T/--trim` also does not add the prefix for missing ranks lower than the current rank. [#82](https://github.com/shenwei356/taxonkit/issues/82)
+        - New flag `-s/--miss-rank-repl-suffix` to set the suffix for estimated taxon names. [#85](https://github.com/shenwei356/taxonkit/issues/85)
 - [TaxonKit v0.14.2](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.2)
 [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.14.2/total.svg)](https://github.com/shenwei356/taxonkit/releases/tag/v0.14.2)
     - `taxonkit filter`:

diff --git a/doc/docs/tutorial.md b/doc/docs/tutorial.md
@@ -182,6 +182,71 @@ where rank of the closest higher node is still lower than rank cutoff**.
     species   Severe acute respiratory syndrome-related coronavirus
     strain    Severe acute respiratory syndrome coronavirus 2
 
+## Mapping old species names to new ones
+
+Some species names in papers or websites might changed, we can try querying their TaxIds via their old new names
+and then retrieve the new ones.
+
+    cat example/changed_species_names.txt
+    Lactobacillus fermentum
+    Mycoplasma gallinaceum
+
+    #  TaxonKit >= v0.15.1
+    cat example/changed_species_names.txt \
+        | taxonkit name2taxid \
+        | taxonkit lineage -i 2 -n \
+        | cut -f 1,4
+
+    Lactobacillus fermentum Limosilactobacillus fermentum
+    Mycoplasma gallinaceum
+
+Woops, there's no information of `Mycoplasma gallinaceum`.
+Then we check the [taxid-changelog](https://github.com/shenwei356/taxid-changelog).
+
+    zcat taxonkit/taxid-changelog.csv.gz \
+        | csvtk grep -f name -P example/changed_species_names.txt
+        | csvtk cut -f taxid,version,change,name,rank \
+        | csvtk pretty
+
+    taxid   version      change           name                      rank
+    -----   ----------   --------------   -----------------------   -------
+    1613    2013-02-21   NEW              Lactobacillus fermentum   species
+    1613    2016-03-01   ABSORB           Lactobacillus fermentum   species
+    1613    2016-03-01   CHANGE_LIN_LEN   Lactobacillus fermentum   species
+    29556   2013-02-21   NEW              Mycoplasma gallinaceum    species
+    29556   2016-03-01   CHANGE_LIN_LEN   Mycoplasma gallinaceum    species
+    29556   2021-01-01   CHANGE_NAME      Mycoplasma gallinaceum    species
+    29556   2021-01-01   CHANGE_LIN_LIN   Mycoplasma gallinaceum    species
+
+We can see the names are changed. Full changes can be queried with the taxid. e.g.,
+
+    taxid   version      change           change-value   name                        rank
+    -----   ----------   --------------   ------------   -------------------------   -------
+    29556   2013-02-21   NEW                             Mycoplasma gallinaceum      species
+    29556   2016-03-01   CHANGE_LIN_LEN                  Mycoplasma gallinaceum      species
+    29556   2020-09-01   CHANGE_NAME                     Mycoplasmopsis gallinacea   species
+    29556   2020-09-01   CHANGE_LIN_TAX                  Mycoplasmopsis gallinacea   species
+    29556   2021-01-01   CHANGE_NAME                     Mycoplasma gallinaceum      species
+    29556   2021-01-01   CHANGE_LIN_LIN                  Mycoplasma gallinaceum      species
+    29556   2021-09-01   CHANGE_NAME                     Mycoplasmopsis gallinacea   species
+    29556   2021-09-01   CHANGE_LIN_LIN                  Mycoplasmopsis gallinacea   species
+    29556   2023-03-01   CHANGE_LIN_LIN                  Mycoplasmopsis gallinacea   species
+
+
+Then we just use their TaxIds to rertrieve the new names. **The final commands are**:
+
+    zcat taxonkit/taxid-changelog.csv.gz \
+        | csvtk grep -f name -P example/changed_species_names.txt \
+        | csvtk uniq -f taxid \
+        | csvtk cut -f name,taxid \
+        | csvtk del-header \
+        | csvtk csv2tab \
+        | taxonkit lineage -i 2 -n \
+        | cut -f 1,4
+
+    Lactobacillus fermentum Limosilactobacillus fermentum
+    Mycoplasma gallinaceum  Mycoplasmopsis gallinacea
+
 ## Add taxonomy information to BLAST result
 
 An blast result file `blast_result.txt`, where the second column is the accession of matched sequences.

diff --git a/doc/docs/usage.md b/doc/docs/usage.md
@@ -42,7 +42,7 @@ All-in-one command:
 ```text
 TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit
 
-Version: 0.14.2
+Version: 0.15.1
 
 Author: Wei Shen <[email protected]>
 
@@ -75,7 +75,7 @@ Available Commands:
   lca             Compute lowest common ancestor (LCA) for TaxIds
   lineage         Query taxonomic lineage of given TaxIds
   list            List taxonomic subtrees of given TaxIds
-  name2taxid      Convert scientific names to TaxIds
+  name2taxid      Convert taxon names to TaxIds
   profile2cami    Convert metagenomic profile table to CAMI format
   reformat        Reformat lineage in canonical ranks
   taxid-changelog Create TaxId changelog from dump archives
@@ -90,6 +90,8 @@ Flags:
   -j, --threads int       number of CPUs. 4 is enough (default 4)
       --verbose           print verbose information
 
+Use "taxonkit [command] --help" for more information about a command.
+
 ```
 
 ## list
@@ -999,11 +1001,11 @@ Examples:
 Usage
 
 ```text
-Convert scientific names to TaxIds
+Convert taxon names to TaxIds
 
 Attention:
 
-  1. Some TaxIds share the same scientific names, e.g, Drosophila.
+  1. Some TaxIds share the same names, e.g, Drosophila.
      These input lines are duplicated with multiple TaxIds.
 
     $ echo Drosophila | taxonkit name2taxid | taxonkit lineage -i 2 -r -L
@@ -1069,6 +1071,12 @@ Example data
         uncultured murine large bowel bacterium BAC 54B 314101  cellular organisms;Bacteria;environmental samples;uncultured murine large bowel bacterium BAC 54B
         Croceibacter phage P2559Y       1327037 Viruses;Caudovirales;Siphoviridae;unclassified Siphoviridae;Croceibacter phage P2559Y
 
+1. Convert old names to new names.
+
+        $ echo Lactobacillus fermentum | taxonkit name2taxid | taxonkit lineage -i 2 -n | cut -f 1,2,4
+        Lactobacillus fermentum 1613    Limosilactobacillus fermentum
+
+
 1. **Some TaxIds share the same scientific names**, e.g, Drosophila.
 
         $ echo Drosophila \

diff --git a/example/changed_species_names.txt b/example/changed_species_names.txt
@@ -0,0 +1,2 @@
+Lactobacillus fermentum
+Mycoplasma gallinaceum
diff --git a/taxonkit/cmd/name2taxid.go b/taxonkit/cmd/name2taxid.go
@@ -33,12 +33,12 @@ import (
 // name2taxidCmd represents the fx2tab command
 var name2taxidCmd = &cobra.Command{
 	Use:   "name2taxid",
-	Short: "Convert scientific names to TaxIds",
-	Long: `Convert scientific names to TaxIds
+	Short: "Convert taxon names to TaxIds",
+	Long: `Convert taxon names to TaxIds
 
 Attention:
 
-  1. Some TaxIds share the same scientific names, e.g, Drosophila.
+  1. Some TaxIds share the same names, e.g, Drosophila.
      These input lines are duplicated with multiple TaxIds.
 
     $ echo Drosophila | taxonkit name2taxid | taxonkit lineage -i 2 -r -L
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		Lactobacillus fermentum
		Mycoplasma gallinaceum