py-graph-imputation-MLO 0.1.0

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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 RunGrim.py script. You can configure the process using a JSON configuration file. Here is an example of how to run the script:

python src/py-graph-imputation-MLO/RunGrim.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 [e-mail].