superseeker 0.1.dev2

SuperSeeker_Pipeline is a Python library for identifying subclonal evolution in cancer.

SuperSeeker Pipeline

The SuperSeeker pipeline is a Python library for identifying subclonal evolution in cancer. It integrates various tools and scripts to process VCF files, cluster variants using PyClone-VI, and reconstruct subclonal evolutionary trees using SuperSeeker.

Installation

Step 1: Install External Tools

Installing PyClone-VI

PyClone-VI is used for clustering genetic variants. You can install it using Conda:

conda install -c bioconda pyclone-vi

Installing SuperSeeker

SuperSeeker is used for reconstructing the evolutionary history of subclones. You can install it from its source repository:

git clone https://github.com/yiq/SuperSeeker.git
cd SuperSeeker

Use the requirements.txt file to install the necessary Python packages:

pip install -r requirements.txt

Step 3: Install the SuperSeeker Python Package

Finally, install the SuperSeeker Pipeline Python package:

pip install superseeker_pipeline

Usage

To use the SuperSeeker pipeline, you can run the run_pipeline function from the superseeker.pipeline module. Here's an example:

from superseeker.pipeline import run_pipeline

run_pipeline(
    patient='patient1',
    vcf_file='input_file.vcf',
    restarts=100,
    clusters=10
)

License

This project is licensed under the MIT License - see the LICENSE.txt file for details.