DNA Visualization

Deoxyribonucleic acid is a tiny molecule that exists in every cell of our bodies and contains the blueprint for how our bodies grow. It looks like a double helix (a sort of twisted ladder) of pairs of nucleotide molecules: guanine, cytosine, adenine, and thymine. These are represented by the letters G, C, A, and T. DNA is a long molecule; it’s microscopic, but if it were stretched out, its 3 billion base pairs would be 2 meters long! This program is a simple animation of DNA.

The Program in Action

When you run dna.py, the output will look like this:

DNA Animation, by Al Sweigart [email protected]
Press Ctrl-C to quit...
        #G-C#
       #C---G#
      #T-----A#
     #T------A#
    #A------T#
    #G-----C#
     #G---C#
     #C-G#
      ##
     #T-A#
     #C---G#
    #G-----C#
    #G------C#
     #T------A#
      #A-----T#
       #C---G#
        #G-C#
         ##
        #T-A#
       #T---A#
      #A-----T#
--snip--

How It Works

Similar to Project 15, “Deep Cave,” and Project 20, “Digital Stream,” this program creates a scrolling animation by printing strings from the ROWS list. The AT and CG pairs are inserted into each string with the format() string method.

Download Source Code

 1. """DNA, by Al Sweigart [email protected]
 2. A simple animation of a DNA double-helix. Press Ctrl-C to stop.
 3. Inspired by matoken https://asciinema.org/a/155441
 4. View this code at https://nostarch.com/big-book-small-python-projects
 5. Tags: short, artistic, scrolling, science"""
 6.
 7. import random, sys, time
 8.
 9. PAUSE = 0.15  # (!) Try changing this to 0.5 or 0.0.
10.
11. # These are the individual rows of the DNA animation:
12. ROWS = [
13.     #123456789 <- Use this to measure the number of spaces:
14.     '         ##',  # Index 0 has no {}.
15.     '        #{}-{}#',
16.     '       #{}---{}#',
17.     '      #{}-----{}#',
18.     '     #{}------{}#',
19.     '    #{}------{}#',
20.     '    #{}-----{}#',
21.     '     #{}---{}#',
22.     '     #{}-{}#',
23.     '      ##',  # Index 9 has no {}.
24.     '     #{}-{}#',
25.     '     #{}---{}#',
26.     '    #{}-----{}#',
27.     '    #{}------{}#',
28.     '     #{}------{}#',
29.     '      #{}-----{}#',
30.     '       #{}---{}#',
31.     '        #{}-{}#']
32.     #123456789 <- Use this to measure the number of spaces:
33.
34. try:
35.     print('DNA Animation, by Al Sweigart [email protected]')
36.     print('Press Ctrl-C to quit...')
37.     time.sleep(2)
38.     rowIndex = 0
39.
40.     while True:  # Main program loop.
41.         # Increment rowIndex to draw next row:
42.         rowIndex = rowIndex + 1
43.         if rowIndex == len(ROWS):
44.             rowIndex = 0
45.
46.         # Row indexes 0 and 9 don't have nucleotides:
47.         if rowIndex == 0 or rowIndex == 9:
48.             print(ROWS[rowIndex])
49.             continue
50.
51.         # Select random nucleotide pairs, guanine-cytosine and
52.         # adenine-thymine:
53.         randomSelection = random.randint(1, 4)
54.         if randomSelection == 1:
55.             leftNucleotide, rightNucleotide = 'A', 'T'
56.         elif randomSelection == 2:
57.             leftNucleotide, rightNucleotide = 'T', 'A'
58.         elif randomSelection == 3:
59.             leftNucleotide, rightNucleotide = 'C', 'G'
60.         elif randomSelection == 4:
61.             leftNucleotide, rightNucleotide = 'G', 'C'
62.
63.         # Print the row.
64.         print(ROWS[rowIndex].format(leftNucleotide, rightNucleotide))
65.         time.sleep(PAUSE)  # Add a slight pause.
66. except KeyboardInterrupt:
67.     sys.exit()  # When Ctrl-C is pressed, end the program.

Exploring the Program

Try to find the answers to the following questions. Experiment with some modifications to the code and rerun the program to see what effect the changes have.

What happens if you change rowIndex = rowIndex + 1 on line 42 to rowIndex = rowIndex + 2?
What happens if you change random.randint(1, 4) on line 53 to random.randint(1, 2)?
What error message do you get if you set PAUSE = 0.15 on line 9 to PAUSE = -0.15?