diff --git a/CHANGELOG.md b/CHANGELOG.md
index 49799d6..74f31e4 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,7 @@
- `taxonkit create-taxdump`:
- accepts arbitrary ranks [#60](https://github.com/shenwei356/taxonkit/issues/60)
- better handle of taxa with same names.
+ - many flags changed.
- [TaxonKit v0.11.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.11.1)
[](https://github.com/shenwei356/taxonkit/releases/tag/v0.11.1)
- `taxonkit create-taxdump`: fix bug of missing Class rank, contributed by @apcamargo. The flag `--gtdb` was not effected. [#57](https://github.com/shenwei356/taxonkit/issues/57)
diff --git a/doc/docs/download.md b/doc/docs/download.md
index 55a6882..808cacd 100644
--- a/doc/docs/download.md
+++ b/doc/docs/download.md
@@ -6,9 +6,12 @@
## Current Version
-- [TaxonKit v0.11.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.11.1)
-[](https://github.com/shenwei356/taxonkit/releases/tag/v0.11.1)
- - `taxonkit create-taxdump`: fix bug of missing Class rank, contributed by @apcamargo. The flag `--gtdb` was not effected. [#57](https://github.com/shenwei356/taxonkit/issues/57)
+- [TaxonKit v0.12.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.0)
+[](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.0)
+ - `taxonkit create-taxdump`:
+ - accepts arbitrary ranks [#60](https://github.com/shenwei356/taxonkit/issues/60)
+ - better handle of taxa with same names.
+ - many flags changed.
### Please cite
@@ -25,11 +28,11 @@
OS |Arch |File, 中国镜像 |Download Count
:------|:---------|:-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|:-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
-Linux |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.11.1/taxonkit_linux_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_amd64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.11.1/taxonkit_linux_amd64.tar.gz)
-Linux |**arm64**|[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.11.1/taxonkit_linux_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_arm64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.11.1/taxonkit_linux_arm64.tar.gz)
-macOS |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.11.1/taxonkit_darwin_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_amd64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.11.1/taxonkit_darwin_amd64.tar.gz)
-macOS |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.11.1/taxonkit_darwin_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_arm64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.11.1/taxonkit_darwin_arm64.tar.gz)
-Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.11.1/taxonkit_windows_amd64.exe.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_windows_amd64.exe.tar.gz)|[](https://github.com/shenwei356/taxonkit/releases/download/v0.11.1/taxonkit_windows_amd64.exe.tar.gz)
+Linux |**64-bit**|[**taxonkit_linux_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.12.0/taxonkit_linux_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_amd64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.12.0/taxonkit_linux_amd64.tar.gz)
+Linux |**arm64**|[**taxonkit_linux_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.12.0/taxonkit_linux_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_linux_arm64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.12.0/taxonkit_linux_arm64.tar.gz)
+macOS |**64-bit**|[**taxonkit_darwin_amd64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.12.0/taxonkit_darwin_amd64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_amd64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.12.0/taxonkit_darwin_amd64.tar.gz)
+macOS |**arm64** |[**taxonkit_darwin_arm64.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.12.0/taxonkit_darwin_arm64.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_darwin_arm64.tar.gz) |[](https://github.com/shenwei356/taxonkit/releases/download/v0.12.0/taxonkit_darwin_arm64.tar.gz)
+Windows|**64-bit**|[**taxonkit_windows_amd64.exe.tar.gz**](https://github.com/shenwei356/taxonkit/releases/download/v0.12.0/taxonkit_windows_amd64.exe.tar.gz),
[中国镜像](http://app.shenwei.me/data/taxonkit/taxonkit_windows_amd64.exe.tar.gz)|[](https://github.com/shenwei356/taxonkit/releases/download/v0.12.0/taxonkit_windows_amd64.exe.tar.gz)
## Installation
@@ -116,6 +119,12 @@ All-in-one command:
## Release history
+- [TaxonKit v0.12.0](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.0)
+[](https://github.com/shenwei356/taxonkit/releases/tag/v0.12.0)
+ - `taxonkit create-taxdump`:
+ - accepts arbitrary ranks [#60](https://github.com/shenwei356/taxonkit/issues/60)
+ - better handle of taxa with same names.
+ - many flags changed.
- [TaxonKit v0.11.1](https://github.com/shenwei356/taxonkit/releases/tag/v0.11.1)
[](https://github.com/shenwei356/taxonkit/releases/tag/v0.11.1)
- `taxonkit create-taxdump`: fix bug of missing Class rank, contributed by @apcamargo. The flag `--gtdb` was not effected. [#57](https://github.com/shenwei356/taxonkit/issues/57)
diff --git a/doc/docs/usage.md b/doc/docs/usage.md
index 81798d5..f639e60 100644
--- a/doc/docs/usage.md
+++ b/doc/docs/usage.md
@@ -41,7 +41,7 @@ All-in-one command:
```text
TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit
-Version: 0.11.1
+Version: 0.12.0
Author: Wei Shen
@@ -65,7 +65,7 @@ Usage:
Available Commands:
cami-filter Remove taxa of given TaxIds and their descendants in CAMI metagenomic profile
- create-taxdump Create NCBI-style taxdump files for custom taxonomy, e.g., GTDB
+ create-taxdump Create NCBI-style taxdump files for custom taxonomy, e.g., GTDB and ICTV
filter Filter TaxIds by taxonomic rank range
genautocomplete generate shell autocompletion script (bash|zsh|fish|powershell)
lca Compute lowest common ancestor (LCA) for TaxIds
@@ -1483,6 +1483,11 @@ Attentions:
Jerseyvirus SETP3 Salmonella phage SETP7
Jerseyvirus SETP7 Salmonella phage SETP7
+ 3. The generated TaxIds are not consecutive numbers, however some tools like MMSeqs2
+ required this, you can use the script below for convertion:
+
+ https://github.com/apcamargo/ictv-mmseqs2-protein-database/blob/master/fix_taxdump.py
+
Usage:
taxonkit create-taxdump [flags]
diff --git a/taxonkit/cmd/cami-filter.go b/taxonkit/cmd/cami-filter.go
index c777431..67dbbc8 100644
--- a/taxonkit/cmd/cami-filter.go
+++ b/taxonkit/cmd/cami-filter.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/cobra_helper.go b/taxonkit/cmd/cobra_helper.go
index 6cc96c8..aad41f2 100644
--- a/taxonkit/cmd/cobra_helper.go
+++ b/taxonkit/cmd/cobra_helper.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/create-taxdump.go b/taxonkit/cmd/create-taxdump.go
index 4152c84..02edf0a 100644
--- a/taxonkit/cmd/create-taxdump.go
+++ b/taxonkit/cmd/create-taxdump.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
@@ -81,6 +81,11 @@ Attentions:
Jerseyvirus SETP3 Salmonella phage SETP7
Jerseyvirus SETP7 Salmonella phage SETP7
+ 3. The generated TaxIds are not consecutive numbers, however some tools like MMSeqs2
+ required this, you can use the script below for convertion:
+
+ https://github.com/apcamargo/ictv-mmseqs2-protein-database/blob/master/fix_taxdump.py
+
`,
Run: func(cmd *cobra.Command, args []string) {
config := getConfigs(cmd)
diff --git a/taxonkit/cmd/filter.go b/taxonkit/cmd/filter.go
index 4562a90..1df369c 100644
--- a/taxonkit/cmd/filter.go
+++ b/taxonkit/cmd/filter.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/genautocomplete.go b/taxonkit/cmd/genautocomplete.go
index 8dfac7f..d9b4838 100644
--- a/taxonkit/cmd/genautocomplete.go
+++ b/taxonkit/cmd/genautocomplete.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/lca.go b/taxonkit/cmd/lca.go
index 1b3027e..2e3b133 100644
--- a/taxonkit/cmd/lca.go
+++ b/taxonkit/cmd/lca.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/lineage.go b/taxonkit/cmd/lineage.go
index dec95ca..a2919cc 100644
--- a/taxonkit/cmd/lineage.go
+++ b/taxonkit/cmd/lineage.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/list.go b/taxonkit/cmd/list.go
index 82d491f..bff30ce 100644
--- a/taxonkit/cmd/list.go
+++ b/taxonkit/cmd/list.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/logging.go b/taxonkit/cmd/logging.go
index 0f2e821..0f2c8ad 100644
--- a/taxonkit/cmd/logging.go
+++ b/taxonkit/cmd/logging.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/name2taxid.go b/taxonkit/cmd/name2taxid.go
index a48095f..03f00d8 100644
--- a/taxonkit/cmd/name2taxid.go
+++ b/taxonkit/cmd/name2taxid.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/profile2cami.go b/taxonkit/cmd/profile2cami.go
index 4fc88e7..2773231 100644
--- a/taxonkit/cmd/profile2cami.go
+++ b/taxonkit/cmd/profile2cami.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/reformat.go b/taxonkit/cmd/reformat.go
index 2d25607..635e37a 100644
--- a/taxonkit/cmd/reformat.go
+++ b/taxonkit/cmd/reformat.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/root.go b/taxonkit/cmd/root.go
index f1313d5..dfef744 100644
--- a/taxonkit/cmd/root.go
+++ b/taxonkit/cmd/root.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/taxid-changelog.go b/taxonkit/cmd/taxid-changelog.go
index 90b1559..cc90cd6 100644
--- a/taxonkit/cmd/taxid-changelog.go
+++ b/taxonkit/cmd/taxid-changelog.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/util-basic-data.go b/taxonkit/cmd/util-basic-data.go
index 40e311c..f1958ba 100644
--- a/taxonkit/cmd/util-basic-data.go
+++ b/taxonkit/cmd/util-basic-data.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/util-cli.go b/taxonkit/cmd/util-cli.go
index 429ffb9..67ec42d 100644
--- a/taxonkit/cmd/util-cli.go
+++ b/taxonkit/cmd/util-cli.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/util-complex-data.go b/taxonkit/cmd/util-complex-data.go
index b60b8dc..7af944b 100644
--- a/taxonkit/cmd/util-complex-data.go
+++ b/taxonkit/cmd/util-complex-data.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/util-filter.go b/taxonkit/cmd/util-filter.go
index e1d4df4..dd89f79 100644
--- a/taxonkit/cmd/util-filter.go
+++ b/taxonkit/cmd/util-filter.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/util-profile.go b/taxonkit/cmd/util-profile.go
index c3260e9..9a45b76 100644
--- a/taxonkit/cmd/util-profile.go
+++ b/taxonkit/cmd/util-profile.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/util-rank.go b/taxonkit/cmd/util-rank.go
index 568c356..a0bf03d 100644
--- a/taxonkit/cmd/util-rank.go
+++ b/taxonkit/cmd/util-rank.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/util.go b/taxonkit/cmd/util.go
index 1990164..74ae580 100644
--- a/taxonkit/cmd/util.go
+++ b/taxonkit/cmd/util.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/cmd/version.go b/taxonkit/cmd/version.go
index 3942501..1556e8a 100644
--- a/taxonkit/cmd/version.go
+++ b/taxonkit/cmd/version.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
diff --git a/taxonkit/main.go b/taxonkit/main.go
index bdd562c..a456984 100644
--- a/taxonkit/main.go
+++ b/taxonkit/main.go
@@ -1,4 +1,4 @@
-// Copyright © 2016-2021 Wei Shen
+// Copyright © 2016-2022 Wei Shen
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal