a Fast Prophage and Phage Predictor
Reason this release was yanked:
Please use the github version currently
Project description
# PhageBoost Rapid discovery of novel prophages using biological feature engineering and machine learning TBA
## Introduction ![Predictions](fig1a.png) 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" `
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for PhageBoost-0.1.3-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 93c161119c831f38a16f8ff71a873c71f1b939522422fe61d9c1cda2909618c2 |
|
MD5 | 2ccd54854abfb019c945cd6d2e1b66e2 |
|
BLAKE2b-256 | 8d49704b8ebd599c15a538d8060bf6a451bc78aff320017fa41d9f039ba0001a |