genetics-viz 0.1.0

A web-based visualization tool for genetics cohort data

Genetics-Viz 🧬

A web-based visualization tool for genetics cohort data.

Features

• Browse multiple cohorts from a single data directory
• View family structures and pedigree information
• Interactive data tables with sorting and filtering
• Clean, modern web interface built with NiceGUI

Installation

From PyPI (when published)

pip install genetics-viz

From source

# Clone the repository
git clone https://github.com/fcliquet/genetics-viz.git
cd genetics-viz

# Install with uv
uv sync

# Or install with pip
pip install -e .

Usage

# Start the web application
genetics-viz /path/to/data/directory

# With custom host and port
genetics-viz /path/to/data/directory --host 0.0.0.0 --port 8000

# With auto-reload for development
genetics-viz /path/to/data/directory --reload

Data Directory Structure

The data directory should have the following structure:

data_directory/
└── cohorts/
    ├── cohort1/
    │   └── cohort1.pedigree.tsv
    ├── cohort2/
    │   └── cohort2.pedigree.tsv
    └── ...

Pedigree File Format

Pedigree files should be tab-separated with the following columns. The header is optional - if present, it must start with "FID":

With header:

FID IID PAT MAT SEX PHENOTYPE
FAM001 IND001 0 0 M affected

Without header (positional columns):

FAM001 IND001 0 0 M affected

Column	Possible Names (case-insensitive)
Family ID	FID, family_id, familyid, family
Individual ID	IID, individual_id, sample_id, sample
Father ID	PAT, father_id, fatherid, father
Mother ID	MAT, mother_id, motherid, mother
Sex	SEX, gender
Phenotype	PHENOTYPE, affected, status

Development

# Install development dependencies
uv sync --dev

# Run tests
uv run pytest

# Run linter
uv run ruff check .

# Format code
uv run ruff format .

License

MIT License