A pair of simple scripts to generate DNA barcodes with nice properties:
- arbitrary length of code
- a minimum Hamming distance between each code
- a GC content percentage upper and lower bound for each code
- a guarantee that no code will contain runs of longer than three of the same base
- Python 3.6 (though >3.4 may work)
- Numba 0.36
- Numpy > 1.12
Best best is to use an Anaconda python distribution. Anaconda 5.0.1 of Python 3.6 worked out of the box for me.
There are two scripts: generate_barcodes.py and validate_barcodes.py. generate_barcodes.py takes a length and filename, and outputs all possible codes of that length:
$ python generate_barcodes <length> <output file>
Once the potential barcode strings have been generated, you can run validate_barcodes.py to get your barcodes by specifying the file of all possible codes, the name where your barcodes should be written, and how many barcodes you need:
$ python validate_barcodes <input file> <output file> <number of codes>