phynteny-transformer 0.1.2

Phynteny: Synteny-based prediction of bacteriophage genes

Phynteny-Transformer

Phynteny is annotation tool for bacteriophage genomes that integrates protein language models and gene synteny. Phynteny leverages a transformer architecture with attention mechanisms and long short term memory to capture the positional information of genes.

Phynteny takes a genbank file with PHROG annotations as input. If you haven't already annotated your phage(s) with Pharokka and phold go do that and then come right back here!

Dependencies

To run the Phynteny Transformer, you need the following dependencies:

• Python 3.9+
• torch
• numpy
• pandas
• click
• loguru
• BioPython
• transformers
• importlib_resources
• scikit-learn
• tqdm

You can install the dependencies using pip:

Installation

You can install Phynteny Transformer from source

git clone https://github.com/susiegriggo/Phynteny_transformer 
cd Phynteny_transformer 
pip install . 

Pip and conda options coming soon

Install Models

Before you can run phynteny you'll need to install some databases

install_models

If you would like to install them to a specific location

install_models -o <path/to/database_dir>

If this doesn't work you can download the models directly from Zenodo and untar them yourself and point Phynteny to them with the -m flag.

Quick Start

phynteny_transformer  test_data/test_phage.gbk -o test_output

Output

• phynteny_transformer.gbk contains a GenBank format file that has been updated to include annotations generated using Phynteny along with their Phynteny score and confidence.
• phynteny_per_cds_funcions.tsv provides a table of the annotations generated (similar to the pharokka_cds_functions.tsv from Pharokka)

Brief Overview

Advanced Usage

Phynteny Transformer provides an advanced mode for specifying the parameters of a model that you trained yourself. To see all advanced options:

phynteny_transformer --help --advanced

Training Custom Models

Phynteny Transformer allows you to train your own custom models. To train a model, you need to provide a dataset in the required format and specify the training parameters. For more details, refer to the documentation in the train_transformer directory.

Bugs and Suggestions

If you break Phynteny or would like to make any suggestions please open an issue or email me at [e-mail] and I'll try to get back to you.

Wow! how can I cite this?

Preprint available at ...