Set of tools used for metagenomics research project
Project description
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:
art
: wrapper code to use ART-ILLUMINA read simulator package from a jupyter notebook. MUST BE RUN LOCALLY.core
: base classes used accross the packagewandb
: utility classes to open, retrieve, use WandB runs and artifacts accross the project
Submodules cover code written for a specific part of the project
cnn_virus
: all specific code related to the evaluation and improvement of CNN Virus modelarchitecture
: all code related to evaluated and trained architecturesdata
: data processing, iterators and parsing functions to handle datautils
: 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
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