predict-circRNA

How to Run

Run train.py, the result model will be saved to MODEL_DIR/model_xx.ckpt. Log will be saved to MODEL_DIR/train.log.

python ./train.py ACTION -o MODEL_DIR [-c CHECK_POINT --seed RANDOM_SEED]

Parameters

• ACTION: Could be train or test.
• CHECK_POINT: Load a model(modelxxxx.ckpt) to either continue training or test model on validation and compute scores.
• optional RANDOM_SEED: random seed for split training data and validation data

Example

python ./train.py train -o model_1
python ./train.py test -c model_1/model6000.ckpt

Preparation

Please copy file hg19.fa, hsa_hg19_Rybak2015.bed, all_exons.bed into the root directory of this repo.

If you have multiple GPU, set environment varaible CUDA_VISIBLE_DEVICES to index of GPUs you want to use.

Dependecies

Install python3, tensorflow, biopython, scipy, sklearn, tqdm.

pip3 install biopython
pip3 install scipy
pip3 install sklearn
pip3 install tqdm