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v0.12.0
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shenwei356 committed Jun 8, 2022
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1 change: 1 addition & 0 deletions CHANGELOG.md
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- `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)
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25 changes: 17 additions & 8 deletions doc/docs/download.md
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## 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

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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),<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/v0.11.1/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),<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/v0.11.1/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),<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/v0.11.1/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),<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/v0.11.1/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),<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/v0.11.1/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),<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/v0.12.0/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),<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/v0.12.0/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),<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/v0.12.0/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),<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/v0.12.0/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),<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/v0.12.0/taxonkit_windows_amd64.exe.tar.gz)

## Installation

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## 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)
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```text
TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit
Version: 0.11.1
Version: 0.12.0
Author: Wei Shen <[email protected]>
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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
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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]
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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7 changes: 6 additions & 1 deletion taxonkit/cmd/create-taxdump.go
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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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)
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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// Copyright © 2016-2021 Wei Shen <[email protected]>
// Copyright © 2016-2022 Wei Shen <[email protected]>
//
// Permission is hereby granted, free of charge, to any person obtaining a copy
// of this software and associated documentation files (the "Software"), to deal
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