什么是 Motif Logo Generator？

Motif Logo Generator 是一款专为研究人员和生物信息学家设计的专业级实用程序，用于为 DNA 或蛋白质基序创建序列 Logo。作为 Openclaw Skills 生态系统的一部分，它提供了一个流线型、可重复的工作流程，将序列比对转换为视觉表示，其中字母高度代表特定位置的信息含量或频率。

该技能专为精准而构建，提供结构化的执行路径，确保生成的每个产物都伴随着记录在案的假设和清晰的验证。通过利用 logomaker 和 matplotlib 等行业标准库，它提供符合数据可视化科学标准的出版级图形。

下载入口:https://github.com/openclaw/skills/tree/main/skills/aipoch-ai/motif-logo-generator

安装与下载

1. ClawHub CLI

从源直接安装技能的最快方式。

2. 手动安装

将技能文件夹复制到以下位置之一

优先级：工作区 > 本地 > 内置

3. 提示词安装

将此提示词复制到 OpenClaw 即可自动安装。

Motif Logo Generator 应用场景

• 为基因组研究从 FASTA 文件创建 DNA 结合位点可视化。
• 分析蛋白质家族的氨基酸保守性以识别功能域。
• 为学术出版物和演讲生成高分辨率的 SVG 或 PDF 资产。
• 作为大型生物信息学数据流水线的一部分，自动生成序列 Logo。

1. 该技能确认用户目标并验证输入，包括源 FASTA 文件或原始序列字符串。
2. 验证序列类型（DNA 或蛋白质）并检查任何特定的样式约束，如配色方案或尺寸。
3. 内部脚本使用 pandas 和 numpy 将序列数据解析为结构化格式。
4. 计算 DNA 的信息含量（bits）或蛋白质序列的相对频率。
5. 工具生成序列 Logo 堆栈并将最终图形导出到指定的输出路径。
6. 返回结构化结果，详细说明工作流程、假设以及执行期间识别的任何风险。

Motif Logo Generator 配置指南

要在您的环境中安装 Motif Logo Generator，请导航到技能目录并安装必要的依赖项：

cd ~/.openclaw/workspace/skills/motif-logo-generator
pip install -r requirements.txt

您可以通过对主脚本运行解析检查来验证安装：

python -m py_compile scripts/main.py

Motif Logo Generator 数据架构与分类体系

该技能通过特定的输入参数管理数据并生成结构化的视觉输出。以下是此 Openclaw Skills 条目的元数据分类：

name: motif-logo-generator description: Generate publication-quality sequence logos for DNA or protein motifs. license: MIT skill-author: AIPOCH

Motif Logo Generator

Generate sequence logos for DNA or protein motifs to visualize conserved positions.

When to Use

• Use this skill when the task is to Generate publication-quality sequence logos for DNA or protein motifs.
• Use this skill for data analysis tasks that require explicit assumptions, bounded scope, and a reproducible output format.
• Use this skill when you need a documented fallback path for missing inputs, execution errors, or partial evidence.

Key Features

• Scope-focused workflow aligned to: Generate publication-quality sequence logos for DNA or protein motifs.
• Packaged executable path(s): scripts/main.py.
• Structured execution path designed to keep outputs consistent and reviewable.

Dependencies

See ## Prerequisites above for related details.

• Python: 3.10+. Repository baseline for current packaged skills.
• numpy: unspecified. Declared in requirements.txt.

Example Usage

See ## Usage above for related details.

cd "20260318/scientific-skills/Data Analytics/motif-logo-generator"
python -m py_compile scripts/main.py
python scripts/main.py --help

Example run plan:

1. Confirm the user input, output path, and any required config values.
2. Edit the in-file CONFIG block or documented parameters if the script uses fixed settings.
3. Run python scripts/main.py with the validated inputs.
4. Review the generated output and return the final artifact with any assumptions called out.

Implementation Details

See ## Workflow above for related details.

• Execution model: validate the request, choose the packaged workflow, and produce a bounded deliverable.
• Input controls: confirm the source files, scope limits, output format, and acceptance criteria before running any script.
• Primary implementation surface: scripts/main.py.
• Parameters to clarify first: input path, output path, scope filters, thresholds, and any domain-specific constraints.
• Output discipline: keep results reproducible, identify assumptions explicitly, and avoid undocumented side effects.

Quick Check

Use this command to verify that the packaged script entry point can be parsed before deeper execution.

python -m py_compile scripts/main.py

Audit-Ready Commands

Use these concrete commands for validation. They are intentionally self-contained and avoid placeholder paths.

python -m py_compile scripts/main.py
python scripts/main.py --help

Workflow

1. Confirm the user objective, required inputs, and non-negotiable constraints before doing detailed work.
2. Validate that the request matches the documented scope and stop early if the task would require unsupported assumptions.
3. Use the packaged script path or the documented reasoning path with only the inputs that are actually available.
4. Return a structured result that separates assumptions, deliverables, risks, and unresolved items.
5. If execution fails or inputs are incomplete, switch to the fallback path and state exactly what blocked full completion.

Installation

cd /Users/z04030865/.openclaw/workspace/skills/motif-logo-generator
pip install -r requirements.txt

Dependencies:

• logomaker - Generate publication-quality sequence logos
• pandas - Data manipulation for sequence alignment
• numpy - Numerical operations
• matplotlib - Visualization backend

Quick Start

# Generate logo from FASTA file
python scripts/main.py --input sequences.fasta --output logo.png --type dna

# Generate logo from raw sequences
python scripts/main.py --sequences "ACGT
ACCT
AGGT" --output logo.png --type dna

# Protein sequences with custom styling
python scripts/main.py --input proteins.fasta --output logo.pdf --type protein --title "Conserved Domain"

Usage

Python API

from motif_logo_generator import generate_logo

# From file
logo = generate_logo(
    input_file="sequences.fasta",
    seq_type="dna",
    output_path="logo.png",
    title="My Motif"
)

# From sequences list
sequences = [
    "ACGTAGCT",
    "ACGTAGCT",
    "ACCTAGCT",
    "ACGTAGTT"
]
logo = generate_logo(
    sequences=sequences,
    seq_type="dna",
    output_path="logo.png"
)

Command Line

python scripts/main.py [OPTIONS]

Required:
  --input PATH       Input FASTA file (or use --sequences)
  --sequences TEXT   Raw sequences separated by newline (or use --input)
  --output PATH      Output file path (.png, .pdf, .svg)

Optional:
  --type {dna,protein}   Sequence type (default: dna)
  --title TEXT           Logo title
  --width INT            Figure width in inches (default: 10)
  --height INT           Figure height in inches (default: 3)
  --colorscheme TEXT     Color scheme (default: classic)
                         DNA: classic, base_pairing
                         Protein: chemistry, hydrophobicity, classic

Output

Generates a sequence logo showing:

• Letter height = information content (conservation)
• Letter stack = frequency at each position
• Y-axis: bits (information content) for DNA, or relative frequency for protein

Example

Input (FASTA):

>seq1
ACGT
>seq2
ACGT
>seq3
ACCT
>seq4
AGGT

Output: Logo with position 2 showing C/G variability and other positions conserved.

Risk Assessment

Security Checklist

• No hardcoded credentials or API keys
• No unauthorized file system access (../)
• Output does not expose sensitive information
• Prompt injection protections in place
• Input file paths validated (no ../ traversal)
• Output directory restricted to workspace
• Script execution in sandboxed environment
• Error messages sanitized (no stack traces exposed)
• Dependencies audited

Prerequisites

# Python dependencies
pip install -r requirements.txt

Evaluation Criteria

Success Metrics

• Successfully executes main functionality
• Output meets quality standards
• Handles edge cases gracefully
• Performance is acceptable

Test Cases

1. Basic Functionality: Standard input → Expected output
2. Edge Case: Invalid input → Graceful error handling
3. Performance: Large dataset → Acceptable processing time

Lifecycle Status

• Current Stage: Draft
• Next Review Date: 2026-03-06
• Known Issues: None
• Planned Improvements:
  • Performance optimization
  • Additional feature support

Output Requirements

Every final response should make these items explicit when they are relevant:

• Objective or requested deliverable
• Inputs used and assumptions introduced
• Workflow or decision path
• Core result, recommendation, or artifact
• Constraints, risks, caveats, or validation needs
• Unresolved items and next-step checks

Error Handling

• If required inputs are missing, state exactly which fields are missing and request only the minimum additional information.
• If the task goes outside the documented scope, stop instead of guessing or silently widening the assignment.
• If scripts/main.py fails, report the failure point, summarize what still can be completed safely, and provide a manual fallback.
• Do not fabricate files, citations, data, search results, or execution outcomes.

Input Validation

This skill accepts requests that match the documented purpose of motif-logo-generator and include enough context to complete the workflow safely.

Do not continue the workflow when the request is out of scope, missing a critical input, or would require unsupported assumptions. Instead respond:

motif-logo-generator only handles its documented workflow. Please provide the missing required inputs or switch to a more suitable skill.

Response Template

Use the following fixed structure for non-trivial requests:

1. Objective
2. Inputs Received
3. Assumptions
4. Workflow
5. Deliverable
6. Risks and Limits
7. Next Checks

If the request is simple, you may compress the structure, but still keep assumptions and limits explicit when they affect correctness.