Motif Logo Generator

Source: https://github.com/aipoch/medical-research-skills

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\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:

• 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