virushostinteractionpredictor 0.0.2

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Virus Host Infection Predictor (VHIP)

Introduction

Goal: Predict hosts for virus of interest from sequence data (fasta files)
Input: Sequences for viruses and hosts of interest and the blast results between viruses and hosts, and between viruses and spacers.
Output: Predictions and score for each virus-host pair. This can be used to plot virus-host infection network.

Requirements

Before the tool can be used, you will need to:

1. Create a virus and a host directory. The virus and host sequences need to be in separate folders. Each fasta file should only represent 1 host or virus.
2. Run blastn between viruses and hosts. Also run CRISPRCasFinder on hosts sequences, then blastn between viruses and the spacers (output of CRISPRCasFinder).
3. Create a conda environment named vhip with the modules/packages that are in the requirements.txt file.

Tutorial

A tutorial is included in the tutorials/ folder, with a test dataset. The test dataset include sequences for hosts, viruses, and the blastn files (viruses against spacers, and viruses against host sequences).