PhaVIP is a python library for phage protein annotation. It has two functions. First, it can classify a protein into either phage virion protein (PVPs) or non-PVPs (binary classification task). Second, it can assign a more detailed annotation for predicted PVPs, such as major capsid, major tail, and portal (multi-class classification task).

PhaVIP is based on chaos game representation and Vision Transformer model. This GitHub is the local version of PhaVIP. The webserver of PhaVIP is avaliable via server version.

In addition, we provide many other phage-related analysis tools, such as phage identification, taxonomy classification, lifestyle prediction, and host prediction. Feel free to check them out on our website PhaBOX.

Overview

Required Dependencies

Detailed package information can be found in phavip.yaml

If you want to use the gpu to accelerate the program please install the packages below:

• cuda
• Pytorch-gpu

Search pytorch to find the correct cuda version based on your computer.

Quick install

Note: we suggest you to install all the package using conda (both miniconda and Anaconda are ok).

After cloning this respository, you can use anaconda to install the phavip.yml. This will install all packages you need with cpu mode. The command is: conda env create -f phavip.yml -n phavip

Once installed, you only need to activate your 'phavip' environment before using phavip in the next time.

conda activate phavip

Usage

Run all pipelines in one command:

python run_PhaVIP.py [--filein INPUT_FA] [--threads NUM_THREAD] [--type IN_TYPE] [--task TASK] [--tool TOOL_PTH] [--root ROOT_PTH] [--mid MID_PTH] [--out OUTPUT_PTH] 

Options

  --filein INPUT_FA
                        The path of your input fasta file.
  --threads NUM_THREAD
                        Number of threads to run PhaMer (default 8)
  --type IN_TYPE
                        Input type of the fasta: protein or dna (default protein)  
  --task TASK
                        Task: binary or multi (default binary)  
  --tool TOOL_PTH
                        The folder where you downlod PhaVIP (default PhaVIP/)
  --root ROOT_PTH
                        The folder you want to store the outputs of PhaVIP (default user_0/)
  --out OUTPUT_PTH
                        The output folder under root. All the prediction will be stored in this folder. (default out/)
  --mid MID_PTH
                        The midfolder under root. All the intermediate files will be stored in this folder. (default midfolder/)

Example

Prediction on the example dna file under PhaVIP folder:

python run_PhaVIP.py --filein test_contigs.fa --threads 8 --type dna --task binary --tool ./ --root sample_test/ --mid midfolder/ --out out/

OR protein file:

python run_PhaVIP.py --filein test_protein.fa --threads 8 --type protein --task binary --tool ./ --root sample_test/ --mid midfolder/ --out out/

Prediction on your data file out of PhaVIP folder:

python run_PhaVIP.py --filein PATH/TO/FASTA/test_contigs.fa --threads 8 --type dna --task binary --tool PATH/TO/PhaVIP --root ~/user_0/ --mid midfolder/ --out out/

References

ArXiv version: Shang, J., Peng, C., Tang, X., & Sun, Y. (2023). PhaVIP: Phage VIrion Protein classification based on chaos game representation and Vision Transformer. arXiv preprint arXiv:2301.12422. ArXiv Link: paper

Contact

If you have any questions, please email us: jyshang2-c@my.cityu.edu.hk