https://github.com/robaina/deepprozyme
https://github.com/robaina/deepprozyme
Last synced: 12 months ago
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- Host: GitHub
- URL: https://github.com/robaina/deepprozyme
- Owner: Robaina
- Created: 2024-02-02T20:40:29.000Z (over 2 years ago)
- Default Branch: main
- Last Pushed: 2024-02-08T10:28:21.000Z (over 2 years ago)
- Last Synced: 2025-06-19T09:12:23.233Z (12 months ago)
- Language: Jupyter Notebook
- Size: 91 MB
- Stars: 0
- Watchers: 1
- Forks: 0
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
#DeepECtransformer
##Procedure
**Note**:
This source code was developed in Linux, and has been tested in Ubuntu 16.04 with Python 3.6.
1. Clone the repository
git clone https://github.com/kaistsystemsbiology/DeepProZyme.git
2. Create and activate virtual environment (takes 5~10 min)
conda env create -f environment.yml
conda activate deepectransformer
3. To use gpus properly, install the pytorch and cuda for your gpus. This code was tested on pytorch=1.7.0 using cuda version 10.2
##Example
- Run DeepECtransformer (takes < 1 min)
python run_deepectransformer.py -i ./example/mdh_ecoli.fa -o ./example/results -g cpu -b 128 -cpu 2
python run_deepectransformer.py -i ./example/mdh_ecoli.fa -o ./example/results -g cuda:3 -b 128 -cpu 2