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Install in OpenClaw
/install blast-species-identification
Description
提供基于BLAST的FASTA序列和OTU表Top ASV的物种注释，支持映射文件、延迟设置和断点续传功能。
README (SKILL.md)
BLAST 物种注释工具技能
描述
提供BLAST物种注释工具的使用指南和快速调用功能。包含两个主要工具：
blast_annotation_tool.py- 对指定FASTA序列进行BLAST注释top_asv_blast.py- 从OTU表提取Top ASV并进行BLAST注释
安装依赖
pip install biopython
工具一：blast_annotation_tool.py
基本用法
# 基本用法：输入FASTA文件和输出目录
python3 blast_annotation_tool.py sequences.fasta results/
# 使用序列ID到样本名的映射文件
python3 blast_annotation_tool.py sequences.fasta results/ --mapping mapping.csv
# 跳过已存在的结果（断点续传）
python3 blast_annotation_tool.py sequences.fasta results/ --skip-existing
参数说明
input: 输入FASTA文件路径 (必填)output: 输出目录路径 (必填)--mapping, -m: 序列ID到样本名的映射文件 (CSV格式)--delay, -d: 每次BLAST请求之间的延迟秒数 (默认: 3)--hits, -n: 每个样本保留的BLAST hits数量 (默认: 10)--skip-existing, -s: 跳过已存在的结果文件 (默认: False)
工具二：top_asv_blast.py
基本用法
# 基本用法
python3 top_asv_blast.py taxa_table.xls rep.fasta results/
# 跳过已存在的结果（断点续传）
python3 top_asv_blast.py taxa_table.xls rep.fasta results/ --skip-existing
# 自定义参数
python3 top_asv_blast.py taxa_table.xls rep.fasta results/ --delay 5 --hits 20
参数说明
otu_table: OTU表文件 (.xls, .tsv, .csv) (必填)fasta: 代表性序列FASTA文件 (必填)output: 输出目录路径 (必填)--top-n, -n: 每个样本提取前N个ASV (默认: 1)--delay, -d: 每次BLAST请求之间的延迟秒数 (默认: 3)--hits: 每个ASV保留的BLAST hits数量 (默认: 10)--skip-existing, -s: 跳过已存在的结果文件 (默认: False)
输入文件格式
FASTA文件
>ASV1
TAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAG...
>ASV2
TAGGGAATCTTCCGCAATGGACGAAAGTCTGACGGAGCAACGCCGCGTGAG...
映射文件 (可选)
CSV格式，第一列为序列ID，第二列为样本名：
ASV1,D1-8
ASV2,J2-8
ASV3,D3-8
OTU表格式
- 第一列：ASV/OTU ID
- 中间列：样本序列计数（支持重复样本自动合并）
- 最后一列：Taxonomy注释
输出文件
- 每个样本的BLAST结果CSV文件
- 汇总表 (blast_summary.csv)
- Top ASV信息表 (top_asv_info.csv)
注意事项
- 需要网络连接访问NCBI BLAST服务
- 每次比对可能需要几秒到几十秒
- 建议使用
--delay参数避免请求过于频繁 - 使用
--skip-existing可实现断点续传
快速调用
当您需要进行BLAST物种注释时，只需说：
- "使用blast注释工具"
- "运行top asv blast"
- "BLAST物种注释指南"
我会为您提供详细的参数说明和使用方法。
Usage Guidance
This skill appears to do exactly what it claims: extract ASV sequences from FASTA/OTU inputs, send them to NCBI BLAST via Biopython, and write CSV results. Before installing or running, check: (1) confirm the filename mismatch (SKILL.md references blast_annotation_tool.py but the repository has blast_annotation.py) and adjust calls accordingly; (2) you will transmit sequence data to NCBI—ensure this is acceptable for privacy/compliance; (3) install Biopython (pip install biopython) and be mindful of NCBI rate limits (use --delay); (4) inspect the hardcoded SAMPLE_TOP_ASV mapping in blast_annotation.py — it may be specific to a dataset and could need updating for your data. If you need the skill to run without network access, it will not work because it relies on NCBI's online qblast service.
Capability Analysis
Type: OpenClaw Skill
Name: blast-species-identification
Version: 1.0.0
The skill bundle provides legitimate bioinformatics tools for species identification using the NCBI BLAST service. The Python scripts (blast_annotation.py and top_asv_blast.py) use the standard Biopython library to perform online sequence alignments and process the results into CSV reports, with appropriate rate-limiting delays. No evidence of data exfiltration, malicious execution, or prompt injection was found.
Capability Assessment
Purpose & Capability
The skill description (BLAST-based species annotation) matches the included Python scripts which call NCBI BLAST via Biopython. Minor inconsistency: SKILL.md refers to 'blast_annotation_tool.py' while the repository provides 'blast_annotation.py' — the filename mismatch should be verified but does not imply malicious behavior.
Instruction Scope
SKILL.md instructs reading FASTA/OTU files and calling BLAST; the scripts read those files, run NCBIWWW.qblast, parse results, and write CSV summaries. They do not access unrelated system files, environment variables, or external endpoints beyond NCBI BLAST.
Install Mechanism
No automated install spec is provided (instruction-only). SKILL.md asks users to 'pip install biopython', which is appropriate. There is no download/extract of remote code in the install step; included scripts will run locally.
Credentials
The skill requires no credentials or environment variables. Network access to NCBI BLAST is necessary and expected for the stated purpose. No unrelated secrets, keys, or config paths are requested.
Persistence & Privilege
The skill does not request permanent presence (always:false) and does not modify other skills or system-wide configuration. It runs as a local script when invoked.
How to Use
- Make sure OpenClaw is installed (local or Docker)
- Run the install command in chat:
/install blast-species-identification - After installation, invoke the skill by name or use
/blast-species-identification - Provide required inputs per the skill's parameter spec and get structured output
Version History
v1.0.0
Initial release of BLAST 物种注释工具技能:
- 提供两大工具脚本（blast_annotation_tool.py 和 top_asv_blast.py）的详细使用指南。
- 支持对FASTA序列或OTU表中的Top ASV进行BLAST注释，含常用参数（如批量处理、断点续传、延迟控制等）。
- 详细说明输入输出文件格式、依赖安装方式和注意事项。
- 支持用户通过自然语言快速调用和获取使用指南。
Metadata
Frequently Asked Questions
What is species_identification_sequence_blast_annotation_tool?
提供基于BLAST的FASTA序列和OTU表Top ASV的物种注释，支持映射文件、延迟设置和断点续传功能。 It is an AI Agent Skill for Claude Code / OpenClaw, with 166 downloads so far.
How do I install species_identification_sequence_blast_annotation_tool?
Run "/install blast-species-identification" in the OpenClaw or Claude Code chat to install it in one step — no extra setup required.
Is species_identification_sequence_blast_annotation_tool free?
Yes, species_identification_sequence_blast_annotation_tool is completely free, licensed under MIT-0. You can download, install and use it at no cost.
Which platforms does species_identification_sequence_blast_annotation_tool support?
species_identification_sequence_blast_annotation_tool is cross-platform and runs anywhere OpenClaw / Claude Code is available (cross-platform).
Who created species_identification_sequence_blast_annotation_tool?
It is built and maintained by Dong Zhao (@zd200572); the current version is v1.0.0.
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