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。
Install
$ agentstack add skill-onescience-ai-oneskills-python-bio-toolkit ✓ scanned · ✓ verified, works with Claude Code, Cursor, and more.
Security review
✓ PassedNo issues found. Passed automated security review. · v0.1.0 How review works →
- ✓ Prompt-injection patterns
- ✓ Secret / credential exfiltration
- ✓ Dangerous shell & filesystem operations
- ✓ Untrusted network calls
- ✓ Known-malicious package signatures
What it can access
- ✓ Network access No
- ✓ Filesystem access No
- ✓ Shell / process execution No
- ✓ Environment & secrets No
- ✓ Dynamic code execution No
From automated source analysis of v0.1.0. “Used” means the capability is present in the source — more access means more to trust, not that it’s unsafe.
Verified badge
Passed review? Show it. Paste this badge into your README, it links to the public security report.
Links to your public security report.[](https://agentstack.voostack.com/security/report/skill-onescience-ai-oneskills-python-bio-toolkit) Reliability & compatibility
Declared compatibility
Compatibility is declared by the source manifest. End-to-end runtime verification is coming, see below.
We're building live execution health for every listing: tool-call success rate, median latency, uptime, and last-checked timestamps, measured, not self-reported. It isn't live yet, so we don't show numbers we can't stand behind.
How agent discovery & health will work →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
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
- Source: onescience-ai/OneSkills
- License: MIT
Install and usage instructions live in the source repository linked above.
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Versions
- v0.1.0 Imported from the upstream source.