TempoMAGE

TEMPOral data Prediction of histone Modifications in Accessible GEnome

Dependencies

To train or test TempoMAGE, you need to install the following dependencies:

• tensorflow 2.1.0
• matplotlib
• sklearn
• pandas
• numpy
• Bio
• cython
• pyranges
• mlxtend

Dataset

A dataset is available in the repository, in the dataset directory and it contains the following:

• training_data.tar.xz: this is the training_set that can be used to train the model. this is only used to demonstrate how the model performs from epoch to another.
• testing_data.tar.xz: this is the test set used to test the already saved model.
• tempoMAGE_savedmodel.tar.xz: the saved model that can be used to predict or test the model.

Usage

python3 train_tempoMAGE.py

train_tempoMAGE.py 
     -t/--training_data <full path for the training dataset FILES>
     -o/--output_dir <output directory for plots>
     -e/--epochs <EPOCHS>
     -s/--save <whether or not to save the trained model>

python3 test_tempoMAGE.py

test_tempoMAGE.py 
     -t/--testing_data <full path for the testing dataset FILES>
     -o/--output_dir <output directory for plots>
     -m/--model <full path for the model already trained>

Train TempoMAGE on training data

To train the model on the training set, extract training_data.tar.xz and use the following command:

python3 train_tempoMAGE.py \
    -t training_data/ \
    -o output_dir/ \
    -e 50 \
    -s yes

Test TempoMAGE on test data

To test the already saved model, extract testing_data.tar.xz and tempoMAGE_savedmodel.tar.xz and use the following command:

python3 test_tempoMAGE.py \
    -t testing_data/ \
    -o out_test/ \
    -m tempoMAGE_savedmodel/