Metadata-Version: 2.1
Name: PhageBoost
Version: 0.1.6
Summary: a Fast Prophage and Phage Predictor
Home-page: https://github.com/ku-cbd/PhageBoost
Author: Kimmo Sirén and Thomas Sicheritz-Pontén
Author-email: kkpsiren@gmail.com
License: UNKNOWN
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 -y -n PhageBoost-env python=3.7 
        conda activate PhageBoost-env
        pip install PhageBoost 
        PhageBoost -h
        ```
        
        #### from GitHub
        
        ```
        conda create -y -n PhageBoost-env python=3.7 
        conda 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" 
        ```
        
Keywords: machine learning,bioinformatics,phage,prophage,bacteria,ngs,metagenomics,wgs,microbiology
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Development Status :: 3 - Alpha 
Classifier: Topic :: Scientific/Engineering
Requires-Python: >=3.6
Description-Content-Type: text/markdown
