metagentools 0.0.9

Set of tools used for metagenomics research project

metagentools

This repo includes the code developed as part of a research project aiming at using deep learning techniques to classify a wide range of corona virus based on NG reads.

The code is structured into general code and submodules:

General code is used across the project and can also be reused for other projects:

1. art: wrapper code to use ART-ILLUMINA read simulator package from a jupyter notebook. MUST BE RUN LOCALLY.
2. core: base classes used accross the package
3. wandb: utility classes to open, retrieve, use WandB runs and artifacts accross the project

Submodules cover code written for a specific part of the project

1. cnn_virus: all specific code related to the evaluation and improvement of CNN Virus model
   • architecture: all code related to evaluated and trained architectures
   • data: data processing, iterators and parsing functions to handle data
   • utils: other utility functions

This is a work in progress, and some functions or modules may be broken. We may or may not be able to provide support depending on the when the support is requested.

Installation:

• pip install metagentools for the stable version

• pip install git+https://github.com/vtecftwy/metagentools.git@main for the latest committed version

Requirements:

• python 3.8 or higher is required for this package
• package tested with python 3.10