Motif Logo Generator

---

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

Key Features

Dependencies

See `## Prerequisites` above for related details.

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.

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:

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\nACCT\nAGGT" --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:

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

| Risk Indicator | Assessment | Level |

|----------------|------------|-------|

| Code Execution | Python/R scripts executed locally | Medium |

| Network Access | No external API calls | Low |

| File System Access | Read input files, write output files | Medium |

| Instruction Tampering | Standard prompt guidelines | Low |

| Data Exposure | Output files saved to workspace | Low |

Security Checklist

Prerequisites

# Python dependencies
pip install -r requirements.txt

Evaluation Criteria

Success Metrics

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

- Performance optimization

- Additional feature support

Output Requirements

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

Error Handling

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.