PredDNAContam 0.0.2

A Machine Learning Model to Estimate Within-Species DNA Contamination.

PredDNAContam

PredDNAContam is a tool for DNA contamination prediction from biosample data.

Input File Format (CSV)

When using PredDNAContam, your input data should be in CSV format with the following columns:

Column	Description
GQ	Genotype quality
DP	Total read depth
AF	Allele frequency
VAF	Variant allele frequency

Example CSV File

The CSV file is generated by extracting the following key features from a VCF (Variant Call Format) file for each variant.

Here’s an example of how the CSV should look after extracting these features:

GQ,DP,AF,VAF
20,47,0.5,0.23
60,25,0.5,0.24
23,55,0.5,0.78

Example config.txt file:

Before running PredDNAContam, you need to configure the paths in the config.txt file. This file contains important directory paths and filenames, which should be set as follows:

input_dir=/path/to/csv_files output_dir=/path/to/output_directory/output_PredDNAcontam model_filename=/path/to/PredDNAContam_model/Random_Forest_Contamination_Model.joblib scaler_filename=/path/to/PredDNAContam_model_scaler/scaler.joblib

Download and Installation

To install PredDNAContam, follow these steps:

1. Download the package You can download the package from PyPI: 👉 PredDNAContam on PyPI 🔗 https://pypi.org/project/PredDNAContam/#files

Download the file: 📂 preddnacontam-0.0.2.tar.gz

2. Extract the package

After downloading, unzip the file:
tar -xvzf preddnacontam-0.0.2.tar.gz
cd preddnacontam-0.0.2

3. Install the package Inside the extracted directory, run:

pip install .

Running PredDNAContam

1. Modify the configuration file Navigate to the scripts directory and update config.txt to set the correct paths for your input files, model, and output directory.

2. Run the tool After configuring the paths, execute PredDNAContam:

PredDNAContam