omics-kit
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
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
- 在
src/omics_kit/<tool>/下写模块，暴露get_parser()和main(argv)； - 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
1 maintainer
Metadata
1 maintainer
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