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shenwei356 · Jan 21, 2021 · 7371fb9 · 7371fb9
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,10 +1,10 @@
 - [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.
-    - new command `taxonkit filter`: filtering taxIDs by taxonomic rank range. [#32](https://github.com/shenwei356/taxonkit/issues/32)
+    - `taxonkit`: **2-3X faster taxonomy data loading**.
+    - new command `taxonkit filter`: **filtering taxIDs by taxonomic rank range**. [#32](https://github.com/shenwei356/taxonkit/issues/32)
     - new command `taxonkit lca`: Computing lowest common ancestor (LCA) for taxIDs.
     - `taxonkit reformat`:
-        - new flag `-P/--add-prefix`: add prefixes for all ranks, single prefix for a rank is defined by flag `--prefix-X`, where `X` may be `k`, `p`, `c`, `o`, `f`, `s`, `S`.
+        - new flag `-P/--add-prefix`: **add prefixes for all ranks**, single prefix for a rank is defined by flag `--prefix-X`, where `X` may be `k`, `p`, `c`, `o`, `f`, `s`, `S`.
         - new flag `-T/--trim`: do not fill missing rank lower than current rank.
     - `taxonkit list`: do not duplicate root node.
 - [TaxonKit v0.6.2](https://github.com/shenwei356/taxonkit/releases/tag/v0.6.2)

diff --git a/README.md b/README.md
@@ -38,7 +38,7 @@
 ## Features
 
 - **Easy to install** ([download](http://bioinf.shenwei.me/taxonkit/download/))
-    - Statically linked executable binaries for multiple platforms (Linux/Windows/macOS, x86/amd64/arm64) 
+    - Statically linked executable binaries for multiple platforms (Linux/Windows/macOS, amd64/arm64) 
     - Light weight and out-of-the-box, no dependencies, no compilation, no configuration*
     - No database building, just download [NCBI taxonomy data](ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz) and uncompress to `$HOME/.taxonkit`
 - **Easy to use** ([usages and examples](http://bioinf.shenwei.me/taxonkit/usage/))
@@ -70,7 +70,7 @@ Subcommand                                                                    |F
 
 1. Getting full lineage for given taxIDs
 
-   <img src="bench/get_lineage/bench.get_lineage.reformat.tsv.png" alt="" width="600" align="center" />
+   <img src="bench/bench.get_lineage.reformat.tsv.png" alt="" width="600" align="center" />
 
 ## Dataset
 

diff --git a/bench/get_lineage/README.md → bench/README.md b/bench/get_lineage/README.md → bench/README.md
diff --git a/...et_lineage/bench.get_lineage.reformat.tsv → bench/bench.get_lineage.reformat.tsv b/...et_lineage/bench.get_lineage.reformat.tsv → bench/bench.get_lineage.reformat.tsv
diff --git a/...ineage/bench.get_lineage.reformat.tsv.png → bench/bench.get_lineage.reformat.tsv.png b/...ineage/bench.get_lineage.reformat.tsv.png → bench/bench.get_lineage.reformat.tsv.png
diff --git a/bench/get_lineage/bench.get_lineage.tsv → bench/bench.get_lineage.tsv b/bench/get_lineage/bench.get_lineage.tsv → bench/bench.get_lineage.tsv
diff --git a/bench/get_lineage/dataset_rename.tsv → bench/dataset_rename.tsv b/bench/get_lineage/dataset_rename.tsv → bench/dataset_rename.tsv
diff --git a/bench/get_lineage/get_lineage.biopython.py → bench/get_lineage.biopython.py b/bench/get_lineage/get_lineage.biopython.py → bench/get_lineage.biopython.py
diff --git a/bench/get_lineage/get_lineage.ete.py → bench/get_lineage.ete.py b/bench/get_lineage/get_lineage.ete.py → bench/get_lineage.ete.py
diff --git a/bench/get_lineage/get_lineage.taxadb.py → bench/get_lineage.taxadb.py b/bench/get_lineage/get_lineage.taxadb.py → bench/get_lineage.taxadb.py
diff --git a/bench/get_lineage/old/README.md → bench/old/README.md b/bench/get_lineage/old/README.md → bench/old/README.md
diff --git a/...ineage/old/bench.get_lineage.reformat.tsv → bench/old/bench.get_lineage.reformat.tsv b/...ineage/old/bench.get_lineage.reformat.tsv → bench/old/bench.get_lineage.reformat.tsv
diff --git a/...ge/old/bench.get_lineage.reformat.tsv.png → bench/old/bench.get_lineage.reformat.tsv.png b/...ge/old/bench.get_lineage.reformat.tsv.png → bench/old/bench.get_lineage.reformat.tsv.png
diff --git a/bench/get_lineage/old/bench.get_lineage.tsv → bench/old/bench.get_lineage.tsv b/bench/get_lineage/old/bench.get_lineage.tsv → bench/old/bench.get_lineage.tsv
diff --git a/bench/get_lineage/old/benchmark.tsv → bench/old/benchmark.tsv b/bench/get_lineage/old/benchmark.tsv → bench/old/benchmark.tsv
diff --git a/bench/get_lineage/old/dataset_rename.tsv → bench/old/dataset_rename.tsv b/bench/get_lineage/old/dataset_rename.tsv → bench/old/dataset_rename.tsv
diff --git a/.../get_lineage/old/get_lineage.biopython.py → bench/old/get_lineage.biopython.py b/.../get_lineage/old/get_lineage.biopython.py → bench/old/get_lineage.biopython.py
diff --git a/bench/get_lineage/old/get_lineage.ete.py → bench/old/get_lineage.ete.py b/bench/get_lineage/old/get_lineage.ete.py → bench/old/get_lineage.ete.py
diff --git a/bench/get_lineage/old/get_lineage.taxadb.py → bench/old/get_lineage.taxadb.py b/bench/get_lineage/old/get_lineage.taxadb.py → bench/old/get_lineage.taxadb.py
diff --git a/bench/get_lineage/old/order.txt → bench/old/order.txt b/bench/get_lineage/old/order.txt → bench/old/order.txt
diff --git a/bench/get_lineage/old/plot.R → bench/old/plot.R b/bench/get_lineage/old/plot.R → bench/old/plot.R
diff --git a/bench/get_lineage/old/plot.sh → bench/old/plot.sh b/bench/get_lineage/old/plot.sh → bench/old/plot.sh
diff --git a/bench/get_lineage/old/run.pl → bench/old/run.pl b/bench/get_lineage/old/run.pl → bench/old/run.pl
diff --git a/bench/get_lineage/old/run_benchmark.sh → bench/old/run_benchmark.sh b/bench/get_lineage/old/run_benchmark.sh → bench/old/run_benchmark.sh
diff --git a/...ineage/old/run_benchmark.sh.benchmark.tsv → bench/old/run_benchmark.sh.benchmark.tsv b/...ineage/old/run_benchmark.sh.benchmark.tsv → bench/old/run_benchmark.sh.benchmark.tsv
diff --git a/...t_lineage/old/run_benchmark.sh.round1.out → bench/old/run_benchmark.sh.round1.out b/...t_lineage/old/run_benchmark.sh.round1.out → bench/old/run_benchmark.sh.round1.out
diff --git a/...t_lineage/old/run_benchmark.sh.round2.out → bench/old/run_benchmark.sh.round2.out b/...t_lineage/old/run_benchmark.sh.round2.out → bench/old/run_benchmark.sh.round2.out
diff --git a/...t_lineage/old/run_benchmark.sh.round3.out → bench/old/run_benchmark.sh.round3.out b/...t_lineage/old/run_benchmark.sh.round3.out → bench/old/run_benchmark.sh.round3.out
diff --git a/bench/get_lineage/old/taxids.big.txt → bench/old/taxids.big.txt b/bench/get_lineage/old/taxids.big.txt → bench/old/taxids.big.txt
diff --git a/bench/get_lineage/old/taxids.medium.txt → bench/old/taxids.medium.txt b/bench/get_lineage/old/taxids.medium.txt → bench/old/taxids.medium.txt
diff --git a/bench/get_lineage/old/taxids.small.txt → bench/old/taxids.small.txt b/bench/get_lineage/old/taxids.small.txt → bench/old/taxids.small.txt
diff --git a/bench/get_lineage/order.txt → bench/order.txt b/bench/get_lineage/order.txt → bench/order.txt
diff --git a/bench/get_lineage/plot.R → bench/plot.R b/bench/get_lineage/plot.R → bench/plot.R
diff --git a/bench/get_lineage/plot.sh → bench/plot.sh b/bench/get_lineage/plot.sh → bench/plot.sh
diff --git a/bench/get_lineage/run.pl → bench/run.pl b/bench/get_lineage/run.pl → bench/run.pl
diff --git a/bench/get_lineage/run_benchmark.sh → bench/run_benchmark.sh b/bench/get_lineage/run_benchmark.sh → bench/run_benchmark.sh
diff --git a/...et_lineage/run_benchmark.sh.benchmark.tsv → bench/run_benchmark.sh.benchmark.tsv b/...et_lineage/run_benchmark.sh.benchmark.tsv → bench/run_benchmark.sh.benchmark.tsv
diff --git a/...h/get_lineage/run_benchmark.sh.round1.out → bench/run_benchmark.sh.round1.out b/...h/get_lineage/run_benchmark.sh.round1.out → bench/run_benchmark.sh.round1.out
diff --git a/...h/get_lineage/run_benchmark.sh.round2.out → bench/run_benchmark.sh.round2.out b/...h/get_lineage/run_benchmark.sh.round2.out → bench/run_benchmark.sh.round2.out
diff --git a/...h/get_lineage/run_benchmark.sh.round3.out → bench/run_benchmark.sh.round3.out b/...h/get_lineage/run_benchmark.sh.round3.out → bench/run_benchmark.sh.round3.out
diff --git a/bench/get_lineage/taxids.big.txt → bench/taxids.big.txt b/bench/get_lineage/taxids.big.txt → bench/taxids.big.txt
diff --git a/bench/get_lineage/taxids.medium.txt → bench/taxids.medium.txt b/bench/get_lineage/taxids.medium.txt → bench/taxids.medium.txt
diff --git a/bench/get_lineage/taxids.small.txt → bench/taxids.small.txt b/bench/get_lineage/taxids.small.txt → bench/taxids.small.txt
diff --git a/doc/docs/download.md b/doc/docs/download.md
@@ -8,14 +8,14 @@
 
 - [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.
-    - new command `taxonkit filter`: filtering taxIDs by taxonomic rank range. [#32](https://github.com/shenwei356/taxonkit/issues/32)
+    - `taxonkit`: **2-3X faster taxonomy data loading**.
+    - new command `taxonkit filter`: **filtering taxIDs by taxonomic rank range**. [#32](https://github.com/shenwei356/taxonkit/issues/32)
     - new command `taxonkit lca`: Computing lowest common ancestor (LCA) for taxIDs.
     - `taxonkit reformat`:
-        - new flag `-P/--add-prefix`: add prefixes for all ranks, single prefix for a rank is defined by flag `--prefix-X`, where `X` may be `k`, `p`, `c`, `o`, `f`, `s`, `S`.
+        - new flag `-P/--add-prefix`: **add prefixes for all ranks**, single prefix for a rank is defined by flag `--prefix-X`, where `X` may be `k`, `p`, `c`, `o`, `f`, `s`, `S`.
         - new flag `-T/--trim`: do not fill missing rank lower than current rank.
     - `taxonkit list`: do not duplicate root node.
-
+    
 Links:
 
 ***Tips***
@@ -24,15 +24,13 @@ Links:
 - run `taxonkit genautocomplete` to update Bash completion !!!
 
 
-OS     |Arch      |File, 中国镜像                                                                                                                                                                              |Download Count
+OS     |Arch      |File, 备用镜像                                                                                                                                                                              |Download Count
 :------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux  |32-bit    |[taxonkit_linux_386.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_linux_386.tar.gz)
-Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_linux_amd64.tar.gz)
-Linux  |**arm64**|[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_linux_arm64.tar.gz)
-macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_darwin_amd64.tar.gz)
-macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_darwin_arm64.tar.gz)
-Windows|32-bit    |[taxonkit_windows_386.exe.tar.gz](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_windows_386.exe.tar.gz)
-Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_windows_amd64.exe.tar.gz)
+Linux  |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_linux_amd64.tar.gz)
+Linux  |**arm64**|[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_linux_arm64.tar.gz)
+macOS  |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_darwin_amd64.tar.gz)
+macOS  |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_darwin_arm64.tar.gz)
+Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.7.0/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/v0.7.0/taxonkit_windows_amd64.exe.tar.gz)
 
 
 ## Installation
@@ -92,6 +90,22 @@ Howto:
           . $bcfile
         done
 
+## Dataset
+
+1. Download and decompress `taxdump.tar.gz`: ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 
+2. Copy `names.dmp`, `nodes.dmp`, `delnodes.dmp` and `merged.dmp` to data directory: `$HOME/.taxonkit`,
+e.g., `/home/shenwei/.taxonkit` ,
+3. Optionally copy to some other directories, and later you can refer to using flag `--data-dir`,
+or environment variable `TAXONKIT_DB`.
+
+All-in-one command:
+
+    wget -c ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz 
+    tar -zxvf taxdump.tar.gz
+
+    mkdir -p $HOME/.taxonkit
+    cp names.dmp nodes.dmp delnodes.dmp merged.dmp $HOME/.taxonkit
+
 ## Previous Versions
 
 - [TaxonKit v0.6.2](https://github.com/shenwei356/taxonkit/releases/tag/v0.6.2)

diff --git a/doc/docs/files/bench.get_lineage.reformat.tsv.png b/doc/docs/files/bench.get_lineage.reformat.tsv.png
@@ -0,0 +1 @@
+../../../bench/get_lineage/bench.get_lineage.reformat.tsv.png
diff --git a/doc/docs/usage.md b/doc/docs/usage.md
@@ -1052,7 +1052,7 @@ Output format (CSV):
                     #   DELETE          deleted
                     #   MERGE           merged into another taxid
                     #   ABSORB          other taxids merged into this one
-                    #   CHANGE_NAME     scientific changed
+                    #   CHANGE_NAME     scientific name changed
                     #   CHANGE_RANK     rank changed
                     #   CHANGE_LIN_LIN  lineage taxids remain but lineage remain
                     #   CHANGE_LIN_TAX  lineage taxids changed

diff --git a/doc/mkdocs.yml b/doc/mkdocs.yml
@@ -4,7 +4,7 @@ pages:
 - Download: download.md
 - Usage: usage.md
 - Tutorial: tutorial.md
-- Benchmark: /bench
+- Benchmark: /bench/
 - Taxid-Changelog: https://github.com/shenwei356/taxid-changelog
 - More tools: https://github.com/shenwei356
 

diff --git a/taxonkit/cmd/taxid-changelog.go b/taxonkit/cmd/taxid-changelog.go
@@ -84,9 +84,9 @@ Output format (CSV):
                     #   DELETE          deleted
                     #   MERGE           merged into another taxid
                     #   ABSORB          other taxids merged into this one
-                    #   CHANGE_NAME     scientific changed
+                    #   CHANGE_NAME     scientific name changed
                     #   CHANGE_RANK     rank changed
-                    #   CHANGE_LIN_LIN  lineage taxids remain but lineage remain
+                    #   CHANGE_LIN_LIN  lineage taxids remain but lineage changed
                     #   CHANGE_LIN_TAX  lineage taxids changed
                     #   CHANGE_LIN_LEN  lineage length changed
     change-value    # variable values for changes:
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1 @@
		../../../bench/get_lineage/bench.get_lineage.reformat.tsv.png