# Bio Python Bio Toolkit

> Python 生信编程工具 skill。用于 Biopython、pysam、cyvcf2、scikit-bio、Bio.PDB、Entrez、BLAST 解析、FASTA/GenBank/PDB/BAM/VCF 编程处理和自定义 Python 生信脚本设计。

- **Type:** Skill
- **Install:** `agentstack add skill-onescience-ai-oneskills-python-bio-toolkit`
- **Verified:** Yes — security-reviewed for prompt injection and unsafe behavior
- **Seller:** [onescience-ai](https://agentstack.voostack.com/s/onescience-ai)
- **Installs:** 0
- **Category:** [Agent Skills](https://agentstack.voostack.com/c/agent-skills)
- **Latest version:** 0.1.0
- **License:** MIT
- **Upstream author:** [onescience-ai](https://github.com/onescience-ai)
- **Source:** https://github.com/onescience-ai/OneSkills/tree/master/skills/onescience-role/assets/bio_domain/analysis-tools/python-bio-toolkit

## Install

```sh
agentstack add skill-onescience-ai-oneskills-python-bio-toolkit
```

Requires the [AgentStack CLI](https://agentstack.voostack.com/docs/cli). Works with Claude Code, Cursor, and any MCP-compatible agent.

## About

# Python 生信工具

## 使用边界

用于包级或脚本级 Python 生信任务。端到端流程仍应由 `workflows` 选择主线。

## 工具选择

- 序列和 GenBank：Biopython SeqIO/SeqRecord/SeqFeature。
- NCBI 查询：Entrez；需要 email/API key 和速率限制。
- BLAST：远程 qblast 或本地 BLAST+，解析 XML/tabular。
- 结构：Bio.PDB 或 MDAnalysis，处理 PDB/mmCIF、chain、residue、RMSD。
- BAM/CRAM：pysam，用于 region fetch、flag/MAPQ、pileup。
- VCF：cyvcf2/pysam.VariantFile，用于 sample genotype、INFO/FORMAT、filter。
- diversity/phylogeny：scikit-bio、Bio.Phylo。

## 交接物

```yaml
tool_family: python-bio
packages:
input_format:
operation:
data_size:
rate_limit_or_external_tool:
expected_output:
execution_entry:
```

## 禁止事项

- 不要用手写正则解析复杂生物格式。
- 不要忽略 NCBI 查询速率和 email/API key。
- 大文件必须用流式或索引访问，不要全量读入。

## Source & license

This open-source skill is cataloged on AgentStack and links to its original source — we do not rehost the code.

- **Author:** [onescience-ai](https://github.com/onescience-ai)
- **Source:** [onescience-ai/OneSkills](https://github.com/onescience-ai/OneSkills)
- **License:** MIT

Install and usage instructions live in the source repository linked above.

## Pricing

- **Free** — Free

## Security capabilities

Automated source analysis of v0.1.0 — what this tool can access:

- **Network access:** no
- **Filesystem access:** no
- **Shell / process execution:** no
- **Environment & secrets:** no
- **Dynamic code execution:** no

*"Yes" means the capability is present in the source — more access means more to trust, not that it is unsafe.*


## Versions

- **0.1.0** — security scan: passed — Imported from the upstream source.

## Links

- Listing page: https://agentstack.voostack.com/l/skill-onescience-ai-oneskills-python-bio-toolkit
- Seller: https://agentstack.voostack.com/s/onescience-ai
- Browse the marketplace: https://agentstack.voostack.com/browse

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Listed on AgentStack — the marketplace for AI agent skills and MCP servers. Every listing is security-reviewed. Creators keep 70%.