├── .gitignore ├── Data ├── raw_data.md └── train_data │ └── readme.md ├── LICENSE ├── README.md ├── codonbert_env.yaml ├── data ├── example_data │ ├── codon_seq.fasta │ ├── codon_seq.npy │ ├── predict.fasta │ └── protein_seq.fasta └── test_data │ └── protein_seq.fasta ├── figures └── 2024.01.24-figure1.jpg ├── models └── kidney_1_1_CodonBert_model_20230726_320_model_param.pt ├── predict.py ├── scripts ├── codon_bert_pytorch.py ├── config_function.py ├── data_formatting.py ├── data_processing.py ├── fasta_to_npy.py └── get_metrics.py └── train.py /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | .logs 3 | *.pyc -------------------------------------------------------------------------------- /Data/raw_data.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/FPPGroup/CodonBERT/HEAD/Data/raw_data.md -------------------------------------------------------------------------------- /Data/train_data/readme.md: -------------------------------------------------------------------------------- 1 | # 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