DeepNup

1.Encoding

DataNup_1, 2 and 3 are all stored in data.zip, you can unzip the file using the following command:

unzip data.zip -d data

• -d data: the folder name you unzip.

Encode the data with the following command：

$python Data_encoded.py -p Fasta_file_Path -f Fasta_filename -o Output_file_Path

• -p Fasta_file_Path: the path of fasta file of raw DNA sequence;
• -f Fasta_filename: the file name of fasta file of raw DNA sequence;
• -o Output_file_Path: the path where the encoding data of DNA sequences is saved.

2.Train the model

Train DeepNup with the following command:

$python training.py -p Pickle_file_Path -o Output_file_Path -e Experiments_Name

• -p Pickle_file_Path: the path of the pickle file;
• -o Output_file_Path: the path where the model is saved;
• -e Experiments_Name: the name of the folder where one model for a specific task is saved.

3.Predict and get results

Predict DeepNup with the following command:

$python predict.py -p Model_file_Path -e Experiments_Name

• -p Model_file_Path: the path where the model was previously saved;
• -e Experiments_Name: the name of the folder where one model for a specific task is saved.