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Pedigree Analysis Framework

A Python-based framework for analyzing pedigrees and estimating inheritance patterns using minimal phenotypic data.

Features

  • Analyze pedigrees using only health status information (affected/unaffected)
  • Estimate inheritance patterns (Autosomal Dominant, Autosomal Recessive, Y-linked)
  • Calculate p-values using Monte Carlo simulation
  • Parallel processing for improved performance on large pedigrees
  • Simple .ped file input format

Installation

git clone https://github.com/yourusername/pedigree-analysis-framework.git
cd pedigree-analysis-framework
pip install -r requirements.txt

Usage

from pedigree import Pedigree, Models

# Load pedigree data
ped = Pedigree()
ped.read_from_file("path/to/your/pedigree.ped")

# Analyze for Autosomal Dominant inheritance
p_value = ped.calc_p_value(Models.AutosomalDominant)
print(f"P-value for Autosomal Dominant inheritance: {p_value}")

# Analyze for Autosomal Recessive inheritance
p_value = ped.calc_p_value(Models.AutosomalRecessive)
print(f"P-value for Autosomal Recessive inheritance: {p_value}")

Input File Format

The framework accepts .ped files with the following format:

ID,Gender,Status,Father,Mother
0,M,U,N,N
1,F,A,N,N
2,M,U,0,1
3,F,A,0,1
  • ID: Unique identifier for each individual
  • Gender: M (Male) or F (Female)
  • Status: A (Affected) or U (Unaffected)
  • Father: ID of the father (N if unknown)
  • Mother: ID of the mother (N if unknown)

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.

License

This project is licensed under the MIT License - see the LICENSE file for details.

Citation

If you use this framework in your research, please cite:

[Your Name]. (2024). Pedigree Analysis Framework. GitHub repository: https://github.com/yourusername/pedigree-analysis-framework

Contact

[Your Name] - [[email protected]]

Project Link: https://github.com/yourusername/pedigree-analysis-framework