PG Exome Depth Tool

Version: 1.0.0

The PG Exome Depth Tool wraps a python graphical interface to call copy-number variations (CNV) from exome-based sequencing data using Exome Depth. This tool guides you through naming your analysis, selecting the folders containing your reference and test BAM files, and then executes an R script to perform the analysis.

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Table of Contents

• Features
• Requirements
• Installation
• Usage
• Project Structure
• Logging
• Troubleshooting
• License
• Contact

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Features

• User-Friendly GUI: Built with Tkinter, the GUI provides simple dialogs to collect user inputs.
• Logging: Execution details (including username and timestamp) are automatically logged for regulatory compliance.
• R Integration: Calls the Exome Depth R script to run the core analysis.
• Interactive Workflow: Guides the user through:
  • Naming the analysis.
  • Selecting the reference folder (with BAM files having an average copy number of 2).
  • Selecting the test folder containing BAM files.
• Results Storage: Analysis results are stored in a dedicated folder within the project.

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Requirements

• Python 3.6+
• R: Must be installed and available on your system’s PATH.
• Non-standard Python Libraries:
  • tkinter (usually included with Python)
  • Pillow (for image handling)
• Operating System: Windows is recommended, given the use of RScript.exe.

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Installation

1. Clone the Repository:

   git clone [https://github.com/yourusername/pg-exomedepth-tool.git](https://github.com/vplagnol/ExomeDepth.git)
   cd pg-exomedepth-tool

2. Set Up a Virtual Environment (Optional but Recommended):

   python -m venv env
   # On Windows:
   env\Scripts\activate
   # On macOS/Linux:
   source env/bin/activate

3. Install Required Python Packages:

   pip install Pillow

4. Ensure R is Installed:

   • Download and install R from CRAN.
   • Make sure RScript.exe is added to your system's PATH so that the Python script can invoke it.

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Usage

1. Run the Application:

   Execute the main Python script from your terminal or command prompt:

   python your_script_name.py

   Replace your_script_name.py with the actual name of your Python file.

2. Follow the On-Screen Prompts:

   • Name Your Analysis: Enter a descriptive name when prompted.
   • Select Reference Folder: Choose the folder that contains your reference BAM files.
   • Select Test Folder: Choose the folder containing the test BAM files for analysis.

3. Analysis Execution:

   • Results are stored in the app_data/cnv_results/ folder within a subfolder named after your analysis.

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Project Structure

pg-exomedepth-tool/
├── app_data/
│   ├── run_logs/         # Contains log files for each execution
│   ├── cnv_results/      # Contains analysis results (CNV outputs)
│   ├── pg_logo.png       # Logo image displayed in the GUI
│   ├── PG_exomedepth.r   # R script for performing the analysis
│   └── path_file.txt     # Stores user inputs (analysis name, folder paths)
├── PG_ExomeDepth_application.py   # Main Python script for running the tool