Description

DeepET model from Li et al.

#TODO upload models to zenodo add code to download models

Requirements

Assuming that you use Miniconda (https://docs.conda.io/en/latest/miniconda.html) or Anaconda (https://www.anaconda.com/) the required packages can be easily installed from the yml file packages.yml. In a terminal execute:

conda env create -f packages.yml
conda activate deepet

Installation

Download repository and unzip (alternatively fork or clone), cd to the project base folder and execute the command below:

pip3 install -e .

If using an anaconda environment you may have to first locate the miniconda pip using whereis.

whereis pip

Locate the appropriate file path (the one that has anaconda and the correct environment in the filepath) and run the modified command. For example:

/home/username/miniconda3/envs/py37/bin/pip install -e .

The library should now be available for loading in all your python scripts.

Usage

from deepet.run_inference import DeepETInference
inf_obj = DeepETInference(model='', layer='')
df = inf_obj.run_inference(filepath='my_sequences.fasta')
df.to_csv('my_sequences_embeddings.tsv', sep='\t')

Valid values for model are: 'ogt' and 'topt'

Valid values for layer are: 'flatten_1', 'dense_1' and 'dense_2'