GeneMap2-Parser ⚡

Overview

This script parses the genemap2.txt file from OMIM and extracts gene-related data, including phenotypes and inheritance information. The parsed output is serialized into a .pickle file for efficient reuse.

Installation

pip install git+https://github.com/OMIM-org/genemap2-parser.git

Usage

parseGeneMap2 -i path/to/genemap2.txt -o path/to/output/

Arguments

• -i, --input_file (Required) Path to genemap2.txt
• -o, --output_path (Optional) Output directory (default: current directory)

Example

parseGeneMap2 -i genemap2.txt -o output_dir/

Output 💾

A output.pickle file containing extracted gene and phenotype data is created in the specified directory.

To read the output:

import pickle
with open("output_dir/output.pickle", "rb") as f:
    data = pickle.load(f)
print(data[:5])  # First 5 entries

Useful Links

• OMIM
• OMIM Downloads

Contributors

• Givron Azim 🚀