Python for Bioinformatics: Python for Simulation: Ulysses

Tuesday, July 21, 2009

Python for Simulation: Ulysses

In the historical remarks for the chapter on Markov Chains in Grinstead and Snell (p. 465), they mention an experiment of Claude Shannon in which a message is generated from a source text by first choosing an initial word in the text, picking (at random) a word which follows that one in the text, and then continuing for a number of cycles. Since each step depends only on the current word, we have a Markov Chain.

I wrote a short Python script to do this. Since I have the text for James Joyce's novel Ulysses (here, from Project Gutenberg), I used that for the source. Some header and footer material was deleted by hand. Here is the output:

i pass on coronation day by the brazen cars
woodshadows floated silently by greed and
behold they wait no she said as i wanted
to win in a cockney accent o thats our hearts
his gaze and squat its loose tobaccoshreds
slanted

Sounds a bit like Joyce, don't you think?

And the full listing:

import random

def loadText():
    FH = open('ulysses.mod.txt','r')
    text = FH.read()
    FH.close()
    text = text.strip().replace('\n',' ')
    text = text.lower()
    alpha = 'abcdefghijklmnopqrstuvwxyz'
    s = alpha + ' '
    tL = [c for c in text if c in s]
    return ''.join(tL).split()
    
def parse(s):
    words = s[:20000]
    D = dict()
    e1 = words.pop(0).strip()
    while words:
        e2 = words.pop(0).strip()
        try:  D[e1].append(e2)
        except KeyError:  D[e1] = [e2]
        e1 = e2
    return D
    
def speak(D,first,N=50):
    L = [first]
    w1 = first
    for i in range(N):
        w2 = random.choice(D[w1])
        L.append(w2)
        w1 = w2
    return ' '.join(L)

def pprint(s):
    i = 0
    n = 40
    while True:
        j = s.find(' ',i+n)
        if j == -1:  
            print s[i+n:]
            break
        if i:  print s[i+1:j]
        else:  print s[:j]
        i = j
    
random.seed(1357)  
text = loadText()
D = parse(text)
result = speak(D,first='i')
pprint(result)