YYC is a DNA storage codec algorithm developed by BGI-research. Briefly, it can transcode two binary sequences into one DNA sequence. This algorithm can help to achieve a high-density, high-feasibility DNA storage based on DNA synthesis.
Environment Configuration
The kit is developed by Python3.5.
In addition, the packages we are calling now is as follows:
- sys
- os
- random
- math
- struct
- datetime
- pickle
Kit Tree Diagram
├── examples // Test module
│ ├── files // Test files
│ │ ├── Mona Lisa.jpg // Mona Lisa.jpg
│ │ ├── United Nations Flag.bmp // United Nations Flag.bmp
│ ├── output // Generated files from handle
│ ├── test_mona_lisa.py // Run YYC using Mona Lisa.jpg
│ ├── test_united_nations_flag.py // Run YYC using United Nations Flag.bmp
├── utils // Util module
│ ├── data_handle.py // Conversion of DNA motifs and binary document
│ ├── index_operator.py // Processing the relationship between index and data
│ ├── log.py // Output the logs in console
│ ├── model_saver.py // Save model to file and load model from file
│ ├── monitor.py // Get the progress situation and the time left
│ ├── validity.py // Determining whether a DNA sequence is easy or not for sequencing and synthesis
├── codec_factory.py // Main calling function
├── yyc.py // YYC (Yin-Yang DNA Storage Code)
├── README.md // Description document of kitIntroduction of Yin-Yang Code
Yin-Yang Code is the algorithm describes the collection of derivative rules reported by Ping et. al. When user need to customize YYC transcoding process, an example of command could be:
yyc.YYC(base_reference=[0, 0, 1, 1], current_code_matrix=[[0, 1, 0, 1],[0, 1, 0, 1],[0, 1, 0, 1],[0, 1, 0, 1]],
support_bases="A", support_spacing=0, max_ratio=0.7, search_count=20)Method of Application
In the encoding process, we first instantiate the method, and then pass the method and the necessary path into codec_factory.
The specific usage is as follows:
import yyc, codec_factory
method = yyc.YYC()
codec_factory.encode(method, input_path="C:\\Mona Lisa.jpg", output_path="C:\\target.dna", model_path="C:\\yyc.pkl")In the decoding process, we first instantiate the method (using path of model file), and then pass the method and the necessary path into entry.
The specific usage (using init method) is as follows:
import codec_factory
codec_factory.decode(input_path="C:\\target.dna", output_path="C:\\target.jpg", model_path="C:\\yyc.pkl")Cite
If you think this repo helps or being used in your research, please consider refer this paper.
Towards Practical and Robust DNA-based Data Archiving by Codec System Named 'Yin-Yang'
Thank you!
