DposFinder is a transformer-based protein language model for phage-encoded depolymerase prediction.
To install DposFinder, follow these steps:
- Clone the repository:
git clone https://github.com/shenyanxiang/DposFinder`
- create a new vertual environment, for example:
cd DposFinder
conda env create -f environment.yml
conda activate DposFinder
- Download trained DposFinder model from the link below and put it into
model
directory:
https://tool2-mml.sjtu.edu.cn/DposFinder/model/Final_DposFinder.pt
or you can retrain DposFinder model with optional params by running:
python ./code/main.py [--FLAGS]
params can be checked by command:
python ./code/main.py -h
Simply use DposFinder to predict depolymerases from protein sequences:
python ./code/main.py --mode predict --data_path ./data --test_data test_set.fasta
Please contact Yanxiang shen at [email protected] for questions.