dnadsl 0.3.1

DNA: a domain-specific language (transcription between UTF-8 text and DNA bases) based on YAML.

DNA

A domain-specific language (transcription between UTF-8 text and DNA bases) based on YAML.

Transcoding

Please refer to coding.py:

DNA_TO_BIN = {
    "A": "00",
    "C": "01",
    "G": "10",
    "T": "11"
}

BIN_TO_DNA = {
    v: k
    for k, v in DNA_TO_BIN.items()
}

DNA_COMPLEMENT = {
    "A": "T",
    "T": "A",
    "C": "G",
    "G": "C"
}

Installation

DNA can be installed from PyPI:

pip install dnadsl

or download the repository and run:

pip install .

as of the repository root folder.

Usage

Run dna --help for help:

$ dna --help
usage: dna [-h] [-m {encode,decode}] [-i INPUT_FILE] [-o OUTPUT_FILE] [-v]

+--------------------------------------------------+
|                        DNA                       |
|            A domain-specific language            |
| (transcription between UTF-8 text and DNA bases) |
|                  based on YAML.                  |
+--------------------------------------------------+

options:
  -h, --help            show this help message and exit
  -m {encode,decode}, --mode {encode,decode}
                        Choose the mode of transcoding.
                        encode: UTF-8 to bases; decode: bases to UTF-8.
                        The default is: encode
  -i INPUT_FILE, --input-file INPUT_FILE
                        The path of the input YAML file.
  -o OUTPUT_FILE, --output-file OUTPUT_FILE
                        The path of the output YAML file.
  -v, --version         Print the version number of dna and exit.

Examples

• Convert UTF-8 text to DNA bases, e.g., run dna -m encode -i input_text.yml -o output_bases.yml:

  • The input UTF-8 text:

    text_utf8: 😄😊
    

  • The output DNA bases:

    text_utf8: 😄😊
    dna:
    positive_strand:
        sequence: TTAAGCTTGCGAGACATTAAGCTTGCGAGAGG
        binary: 11110000 10011111 10011000 10000100 11110000 10011111 10011000 10001010
        text: 😄😊
    negative_strand:
        sequence: AATTCGAACGCTCTGTAATTCGAACGCTCTCC
        binary: 00001111 01100000 01100111 01111011 00001111 01100000 01100111 01110101
        text: "\x0F`g{\x0F`gu"
    

• Convert DNA bases to UTF-8 text, e.g., run dna -m decode -i input_bases.yml -o output_text.yml:

  • The input DNA bases:

    positive_strand: TGAGGCTCGGCATGTTGTGAGATTTTAAGCTTGCAAGTCG
    

  • The output UTF-8 text:

    text_utf8: ❤️🐶
    dna:
    positive_strand:
        sequence: TGAGGCTCGGCATGTTGTGAGATTTTAAGCTTGCAAGTCG
        binary: 11100010 10011101 10100100 11101111 10111000 10001111 11110000 10011111
        10010000 10110110
        text: ❤️🐶
    negative_strand:
        sequence: ACTCCGAGCCGTACAACACTCTAAAATTCGAACGTTCAGC
        binary: 00011101 01100010 01011011 00010000 01000111 01110000 00001111 01100000
        01101111 01001001
        text: "\x1Db[\x10Gp\x0F`oI"
    

Packaging

The binaries are created with PyInstaller:

# Package it on Linux
pyinstaller --name DNA --onefile -p dna dna/__main__.py

# Package it on Windows
pyinstaller --name DNA --onefile --icon python.ico -p dna dna/__main__.py

Copyrights

DNA is a free, open-source software package (distributed under the GPLv3 license). The logo used in README.md is downloaded from Wikimedia Commons. The Python icon is downloaded from python.ico.