VirusHostInteractionPredictor

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VirusHostInteractionPredictor

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Python tool to predict ecological virus-host infection

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# Virus Host Interaction Predictor (VHIP)

[![Test](https://github.com/DuhaimeLab/VirusHostInteractionPredictor/actions/workflows/test.yml/badge.svg?branch=main&event=push)](https://github.com/DuhaimeLab/VirusHostInteractionPredictor/actions/workflows/test.yml)
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## Introduction

VHIP is a machine-learning model that predict virus-microbe interactions (i.e., infection or non-infection) from genomic sequences of viruses and microbes of interest. It leverages virus-microbe coevolution signal that are extracted from genomic sequences. VHIP was trained on lab-verified virus-microbe pairs collected from literature and the NCBI virus database.

You can find more information about the philosophy and performance of VHIP here: https://www.biorxiv.org/content/10.1101/2023.11.03.565433v1

## Installation

This python package can be installed with PyPI

```
pip install virushostinteractionpredictor
```

It is also available through conda-forge.

```
conda config --add channels conda-forge
conda install virushostinteractionpredictor
```

Once installed, you can import the vhip python module. See the `example` folder on how to run the tool.

## Inputs

The inputs for VHIP are sequences for the viruses and hosts of interest. Each file should represent an unique virus/host species. In addition, a blastn between the virus and host sequences, and between viruses and host spacers are needed. If there are no results from the blastn, then the files can be empty.

## Example

An example is included in the `example` folder. It includes virus and microbes sequences, how they should be organized (separate folders), and example blastn files. Make sure you are able to run VHIP on the example before applying to a new dataset.

## Citation

https://www.biorxiv.org/content/10.1101/2023.11.03.565433v1

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