Harvard:Biophysics 101/2007/Notebook:CChi/2007-2-8

Assignment 1, due 2/8/07

Write a python script that generates 10,000 strings of 10 random coinflips (H or T) and outputs the tally of continguous (overlapping) stretches of 2, 3, 4, 5, 6, 7, 8, 9, and 10 H's or T's in that set of 10,000 10-mers.

Code

#!/usr/bin/env python

import random

# make a list of values for each 
tallyH = [0 for i in range(11)]
tallyT = [0 for i in range(11)]

# 10000 trials of 10 flips each
for i in range(10000):
    # Generates random 10-mer of H's and T's
    coinflip = ''.join([random.choice(['H','T']) for n in range (10)])

    # loop to tally up instances of each k-mer (from 2 to 10)
    for k in range(2,11):

        # counts up number of "H" k-mers in this coinflip
        Hsubstr = ''.join(['H' for n in range(k)])     
        Hcount = 0
        pos = coinflip.find(Hsubstr,0)
        while not pos == -1:
            Hcount = Hcount + 1
            pos = coinflip.find(Hsubstr,pos+1)
        tallyH[k] = tallyH[k] + Hcount

        Tsubstr = ''.join(['T' for n in range(k)])
        Tcount = 0
        pos = coinflip.find(Tsubstr,0)
        while not pos == -1:
            Tcount = Tcount + 1
            pos = coinflip.find(Tsubstr,pos+1)
        tallyT[k] = tallyT[k] + Tcount        

# print out the results
print "Head strings"
for i in range(2,11):
    print i, tallyH[i]

print "\nTail strings"
for i in range (2,11):
    print i, tallyT[i]

Output

Head strings
2 22572
3 9968
4 4362
5 1881
6 786
7 315
8 121
9 38
10 5

Tail strings
2 22338
3 9895
4 4362
5 1892
6 804
7 328
8 123
9 41
10 10