a Fast Prophage and Phage Predictor
Project description
PhageBoost
Rapid discovery of novel prophages using biological feature engineering and machine learning
TBA
Introduction
Prophage predictor based on gene features against a background.
Prophages are phages integrated into prokaryotic genomes that drive many aspects of bacterial biology. Their extreme diversity means they are challenging to detect using sequence similarity. We present a novel fast and generalizing machine learning method to facilitate novel phage discovery.
Publications
to be added
Getting Started
Installation
from PyPI
conda create -n PhageBoost-env python=3.7
source activate PhageBoost-env
pip install PhageBoost
PhageBoost -h
from GitHub
conda create -n PhageBoost-env python=3.7
source activate PhageBoost-env
git clone git@github.com:ku-cbd/PhageBoost.git
cd PhageBoost/
python setup.py bdist_wheel
pip install --user .
PhageBoost -h
CLI
PhageBoost -h
PhageBoost -f example/data/NC_000907.fasta.gz -o results
Notebooks
There are basic notebook examples in the notebooks/
These notebooks provide a way how to bring your own genecalls to PhageBoost.
You can connect your PhageBoost kernel to your pre-existing Jupyter via ipykernel:
conda activate PhageBoost
pip install ipykernel
python -m ipykernel install --user --name PhageBoost --display-name "PhageBoost"
Project details
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