Py-Graph-Imputation-MLO

Overview

py-graph-imputation-MLO is a Python package for graph-based imputation of missing data in genetic datasets. It leverages the py-graph-imputation library and provides additional functionality for filtering and processing imputed results.

Installation

To install the package, use the following command:

pip install py-graph-imputation-MLO

Dependencies

The package requires the following dependencies:

• py-graph-imputation
• cython == 0.29.32
• numpy >= 1.20.2
• pandas
• tqdm

These dependencies will be installed automatically when you install the package.

Usage

Running the Imputation

To run the imputation process, use the run_grim.py script. You can configure the process using a JSON configuration file. Here is an example of how to run the script:

python run_grim.py

Configuration

The configuration file should be in JSON format and include the following fields:

• freq_file: Path to the frequency file.
• imputation_in_file: Path to the input file for imputation.
• imputation_out_path: Path to the output directory for imputation results.
• imputation_out_hap_freq_filename: Filename for the haplotype frequency output.
• imputation_out_umug_freq_filename: Filename for the UMUG frequency output.
• imputation_out_umug_pops_filename: Filename for the UMUG populations output.
• imputation_out_hap_pops_filename: Filename for the haplotype populations output.
• imputation_out_miss_filename: Filename for the missing data output.
• output_MUUG: Boolean flag to enable/disable MUUG output.
• output_haplotypes: Boolean flag to enable/disable haplotype output.
• number_of_results: Number of results to output.
• number_of_pop_results: Number of population results to output.

Example Configuration

Here is an example of a minimal configuration file:

{
  "freq_file": "path/to/frequency/file",
  "imputation_in_file": "path/to/input/file",
  "imputation_out_path": "path/to/output/directory",
  "imputation_out_hap_freq_filename": "hap_freq.csv",
  "imputation_out_umug_freq_filename": "umug_freq.csv",
  "imputation_out_umug_pops_filename": "umug_pops.csv",
  "imputation_out_hap_pops_filename": "hap_pops.csv",
  "imputation_out_miss_filename": "miss.csv",
  "output_MUUG": true,
  "output_haplotypes": true,
  "number_of_results": 10,
  "number_of_pop_results": 5
}

License

This project is licensed under the MIT License. See the LICENSE file for more details.

Contact

For any questions or inquiries, please contact Regev Yehezkel Imra at regevel2006@gmail.com.