CRPTS: Predicting Transcription Factor Binding Sites using DNA Shape Features Based on Shared Hybrid Deep Learning Architecture
- To install Keras with Tensorflow backend, please refer to https://keras.io/#installation.
- Tensorflow == 2.1.4
- keras == 2.1.4
- Python 3.10
Clone the repositopry into your working space.
Download the data from https://bitbucket.org/wenxiu/sequence-shape/get/2159e4ef25be.zip Firstly, using encode.sh script to preprocess DNA sequences and their corresponding shape features.
- Usage: bash encode.sh
- 'pbmdata' denotes the path of storing experimental data, e.g. /yourpath/pbmdata.
- Usage: you can excute run.sh script directly, in which you should modify the python command accordingly, e.g.:
python train_val_test_hybrid.py -datadir ./pbmdata/$eachTF/data -run 'shape' -model 'CRPTS' -batchsize 300 -k 5 -params 30 --train
- The command '-run' means 'shape' using four shape features, and the command '-model' can be a choice of {'CRPTS', 'CRPT'}
- Note that you should change the ouput path in the run.sh script, the naming rule is:
'model_' + args.model + '_' + args.run.
- Type the following for details on other optional arguments:
python train_val_test_hybrid.py -h
- If you have any problems, please contact SiguoWang: [email protected]