PhageBoost 0.1.3

# 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 PhageBoost1 python=3.7 && conda activate PhageBoost1 && pip install PhageBoost ` #### from github ` conda create -n PhageBoost python=3.7 && conda activate PhageBoost && git clone git@github.com:ku-cbd/PhageBoost.git && cd PhageBoost/ && python setup.py bdist_wheel && pip install --user . `

### 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" `