CS440
Homework 1 (due Thurs 8/31)
The purpose of this is assignment is for you to familiarize yourself with Python. Example
input files for the programs can be found on the homework section of the course website.
1. Some elementary calculations (40%)
A numerical data set (nums.txt) will be provided as a text file, and your task is to
read each line and calculate the sum, average (x), and standard deviation (σ) of the
line. Write these numbers to a file in tab-delimited format such that Each line in the
output file will contain the sum average standard deviation of the corresponding line
in nums.txt. The name of the input file and output file will be given as command-line
arguments. The standard deviation can be calculated as:
σ=v
u
u
t
1
N
N
X
i=1
(xi−x)2
Write your code in a file named part1.py. Your program for this part should execute
from a linux shell as $python part1.py infile outfile. An example python script is
provided.
Warning: Python distinguishes between integer and float division. Cast a number to
the appropriate type to ensure the correct operation.
Hint: You might find the Python function sum useful.
2. A biological application (60%)
DNA is a complex biological molecule that carries the genetic material for all living
organisms. It is a long molecule composed of the four nucleotides adenine (A), cyto-
sine (C), guanine (G), thymine (T). DNA can therefore be represented as a string of
characters over the alphabet A, C, G, T. Your task for this part is to write a python
module that contains a function that counts the number of times each di-nucleotide
(substring of nucleotides of length = 2) occurs in a DNA sequence. The counts for the
sequence CGTGTGAC, are found in Table 1.
Your function, named dinucleotide count will take the name of a fasta-formatted file
as its only argument and calculate how many times each di-nucleotide occurs. The
function will return a python dictionary whose keys are di-nucleotides, and its values
are a tuple (count, percentage), where count is the number of times a di-nucleotide has
occurred in the file and percentage is the percentage of the di-nucleotide over all records
in the file, rounded to the nearest tenth of a percent. The data file b anthracis.fasta
(the DNA sequences of the proteins in the bacterium bacillus anthracis, a.k.a. anthrax)
has been provided to test your function.
