omics-kit

PyPI Python License

组学数据分析的命令行小工具集，每个工具都是 omics-kit 的一个子命令。

pip install omics-kit
omics-kit                       # 列出所有子命令
omics-kit rna-structure -h      # 单个子命令的参数

子命令

子命令 说明 文档
rna-structure 用 VARNA 画 RNA 二级结构，支持 motif 高亮、RNAcentral/R2DT 直连、RNAfold 折叠 docs/rna-structure.md
rnacentral-fetch 从 RNAcentral 取序列 + R2DT 二级结构，写成 dbn docs/rna-structure.md

上手

# 从 RNAcentral 编号直接出图，并高亮三个 motif
omics-kit rna-structure -r URS00000DE3E2/9606 -o SNORA73A.svg \
    -m "7BM:18-31:#E8DAA6:#93C795" \
    -m "MBM:117-126:#EFB9C6:#93C795" \
    -m "Ψ pocket:143-152,186-192:fill=#AED6EA,outline=#93C795,type=L"

# 复现 Cell 2025 Figure 4A（motif 表已随包分发）
omics-kit rnacentral-fetch -r URS00000DE3E2/9606 -n SNORA73A -o SNORA73A.dbn
omics-kit rna-structure -i SNORA73A.dbn -M SNORA73A_figure4A -o figure4A.png \
    --title "SNORA73A structure" --title-size 14 --resolution 4

SNORA73A

依赖

Python 侧只依赖 termcolor，其余按需：

工具 外部依赖 说明
rna-structure Java 1.6+ 运行 VARNA；jar 首次使用时自动下载到 ~/.cache/omics-kit/varna（可用 $VARNA_JAR 或 --jar 指定）
rna-structure --fold ViennaRNA 只有需要现场折叠时才用到 RNAfold

开发

git clone https://github.com/typekey/omics-kit.git
cd omics-kit
pip install -e .

python3 -m unittest discover -s tests -v            # 全部用例（联网 + 渲染）
OMICS_SKIP_NETWORK=1 python3 -m unittest discover -s tests   # 离线用例
python3 -m build                                    # 构建 wheel/sdist 到 dist/

新增一个子命令

  1. 在 src/omics_kit/<tool>/ 下写模块，暴露 get_parser() 和 main(argv)；
  2. 在 src/omics_kit/cli.py 的 COMMANDS 里加一行（模块路径 + 一句话描述）。

模块是懒加载的，重依赖的工具不会拖慢其它子命令。

发布

打 tag 推上去即可，GitHub Action 会构建并通过 PyPI Trusted Publishing 发布：

git tag v0.1.0 && git push origin v0.1.0

引用

  • VARNA：Darty K, Denise A, Ponty Y. VARNA: Interactive drawing and editing of the RNA secondary structure. Bioinformatics 2009, 25(15):1974-1975.
  • R2DT / RNAcentral：Sweeney BA, et al. R2DT is a framework for predicting and visualising RNA secondary structure using templates. Nat Commun 2021, 12:3494.

License

Apache-2.0

Project links

Data verified by PyPI on Aug 6, 2026
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Avatar for baimocc from gravatar.com baimocc

Credits

Author: Lei Zheng

GitHub Statistics

Data verified by PyPI on Aug 6, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License

Apache Software License (Apache-2.0)

Requires

Python >=3.8

Tags

bioinformatics omics RNA secondary structure VARNA RNAcentral

Classifiers

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