AmplifyP

AmplifyP is a Python rewrite of William Engels's Amplify4, a tool for simulating Polymerase Chain Reaction (PCR). It allows users to predict amplification products (amplicons) from a given DNA template and a set of primers, taking into account the primability and stability of primer binding sites.

Features

• PCR Simulation: Predict potential amplicons based on primer binding properties.
• Scoring System: Calculates primability and stability scores for primer binding sites using customizable weight tables.
• GUI Application: Includes a Tkinter-based graphical user interface for easy interaction.
• Python API: Provides a flexible API for programmatic access to simulation tools.

Installation

To use AmplifyP, clone the repository and ensure you have a compatible Python environment (Python 3.12+).

You probably want to set up your Python virtual environment first:

python -m venv venv
source venv/bin/activate

Then install AmplifyP:

git clone https://github.com/fangfufu/AmplifyP.git
cd AmplifyP
pip install .

Usage

Web Version

You can run AmplifyP directly in your browser without any installation! Visit the live static web app here: https://fangfufu.github.io/AmplifyP/

To test the static site build locally:

./build_static.sh
python -m http.server 23455 -d src/dist

Then open http://localhost:23455 in your browser.

Note: The static site runs Python entirely in the browser via Pyodide. File save/load uses a custom file_handler.js that bridges the Pyodide Web Worker with the main thread for DOM-based file operations.

Graphical User Interface (Local)

To launch the GUI locally as a desktop app:

python src/main.py

The GUI allows you to:

1. Input a template DNA sequence.
2. Add multiple primers.
3. Configure primability and stability cutoffs.
4. Simulate PCR to view potential amplicons.
5. Analyze individual primers to see all potential binding sites.

Python API

You can also use AmplifyP as a library in your Python scripts.

from amplifyp.dna import DNA, Primer, DNAType
from amplifyp.repliconf import Repliconf
from amplifyp.amplicon import AmpliconGenerator
from amplifyp.settings import DEFAULT_SETTINGS

# 1. Define your DNA template and primers
template_seq = "AGCT..."  # Replace with your actual sequence
template = DNA(template_seq, DNAType.LINEAR, name="MyTemplate")

primer_fwd = Primer("AGCT...", name="FwdPrimer")
primer_rev = Primer("TCGA...", name="RevPrimer")

# 2. Initialize the Amplicon Generator
generator = AmpliconGenerator(template)

# 3. Create Replication Configurations for each primer
# This step calculates potential binding sites on the template
conf_fwd = Repliconf(template, primer_fwd, DEFAULT_SETTINGS)
conf_rev = Repliconf(template, primer_rev, DEFAULT_SETTINGS)

# 4. Search for origins (binding sites)
conf_fwd.search()
conf_rev.search()

# 5. Add configurations to the generator
generator.add(conf_fwd)
generator.add(conf_rev)

# 6. Generate amplicons
amplicons = generator.get_amplicons()

for amp in amplicons:
    print(f"Product: {amp.product.name}")
    print(f"Sequence: {amp.product.seq}")
    print(f"Length: {len(amp.product)}")
    print(f"Quality Score: {amp.q_score}")
    print("-" * 20)

Development

Running Tests

To run the unit tests, install pytest and run it from the root of the repository:

pip install pytest pytest-cov
pytest

Attribution

This project is based on the logic and methodology of Amplify4 by William Engels. We aim to preserve the accuracy of the original simulations while providing a modern Python implementation.

License

This project is licensed under the GPL-3.0 License - see the LICENSE file for details.