From 211a869e83932ec6a4d43d28276ac19ba2395bfe Mon Sep 17 00:00:00 2001 From: Wei Shen Date: Wed, 8 Jun 2022 10:23:34 +0800 Subject: [PATCH] v0.12.0 --- CHANGELOG.md | 1 + doc/docs/download.md | 25 +++++++++++++++++-------- doc/docs/usage.md | 9 +++++++-- taxonkit/cmd/cami-filter.go | 2 +- taxonkit/cmd/cobra_helper.go | 2 +- taxonkit/cmd/create-taxdump.go | 7 ++++++- taxonkit/cmd/filter.go | 2 +- taxonkit/cmd/genautocomplete.go | 2 +- taxonkit/cmd/lca.go | 2 +- taxonkit/cmd/lineage.go | 2 +- taxonkit/cmd/list.go | 2 +- taxonkit/cmd/logging.go | 2 +- taxonkit/cmd/name2taxid.go | 2 +- taxonkit/cmd/profile2cami.go | 2 +- taxonkit/cmd/reformat.go | 2 +- taxonkit/cmd/root.go | 2 +- taxonkit/cmd/taxid-changelog.go | 2 +- taxonkit/cmd/util-basic-data.go | 2 +- taxonkit/cmd/util-cli.go | 2 +- taxonkit/cmd/util-complex-data.go | 2 +- taxonkit/cmd/util-filter.go | 2 +- taxonkit/cmd/util-profile.go | 2 +- taxonkit/cmd/util-rank.go | 2 +- taxonkit/cmd/util.go | 2 +- taxonkit/cmd/version.go | 2 +- taxonkit/main.go | 2 +- 26 files changed, 53 insertions(+), 33 deletions(-) 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) [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.11.1/total.svg)](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) -[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.11.1/total.svg)](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) +[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.12.0/total.svg)](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) |[![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/v0.11.1/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) |[![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/v0.11.1/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) |[![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/v0.11.1/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) |[![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/v0.11.1/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)|[![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/v0.11.1/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) |[![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/v0.12.0/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) |[![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/v0.12.0/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) |[![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/v0.12.0/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) |[![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/v0.12.0/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)|[![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/v0.12.0/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) +[![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.12.0/total.svg)](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) [![Github Releases (by Release)](https://img.shields.io/github/downloads/shenwei356/taxonkit/v0.11.1/total.svg)](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