Harvard:Biophysics 101/2007/02/08

Q&A

• Q1: "I keep getting indentation errors when running my python scripts - what's the deal?"
• A1: See 1, 2 for info.

New tasks

• Start thinking about what kind of project you want to work on.
• Read the Python Style Guide by GvR

Solution to Feb 6 Assignment

• Here's my take on the Feb 6 assignment. --smd 12:28, 8 February 2007 (EST)

#!/usr/bin/env python

from random import choice

# create a list to store our results
tally = [0 for i in range(11)]

for i in range(10000):
    # generate a random 10-mer
    coinflip = ''.join([choice('HT') for j in range(10)])

    # tally k-mers in the 10-mer
    for k in range(2,11):
        Hcount = Tcount = 0

        H = ''.join(['H' for n in range(k)]) # k-mer of H's
        pos = coinflip.find(H,0)
        while not pos == -1:
            Hcount = Hcount + 1
            pos = coinflip.find(H,pos+1)

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

        tally[k] = tally[k] + Hcount + Tcount

for i in range(2,11):
    print '%2s: %5d' % (i, tally[i])

• Example output

 2: 45129
 3: 20055
 4:  8776
 5:  3784
 6:  1588
 7:   638
 8:   247
 9:    81
10:    22