Data Organization Programming Assignment #4

CS 241L - Data Organization

Programming Assignment #4
Total points: 100

In this assignment, you will write a simple C program that includes processing input and using
control structures.
1 Extract files from tarball:
Log ino the cs machines. Create a directory for this assignment as follows:
$ cd cs241 ; $ mkdir prog04
$ chmod 700 prog04 ; $ cd prog04
The necessary files are given to you as a compressed tarball. In order to extract the files from this
tarball use the command:
$ tar -xvf programming assignment 4.tar.gz.
This will create the following seven (7) files in your current directory: dnaInput 1, dnaInput 2,
dnaInput 3, dnaInput 4, outputFile 1, outputFile 2, and outputFile 3.
2 Description of the assignment
DNA is the basis of life here on earth. Every living creature is described by their DNA, which is a very,
very long sequence of the bases A, C, G and T. Bioinformatics is a new discipline that uses the power
of computers to analyze biological data, to discover new insights about the mysteries of life. For this
assignment, you will complete a very simple bioinformatics experiment.
1
The input for your program will be a text file consisting of a sequence of DNA bases. Each base can
appear as either a upper-case or as a lowercase letter (i.e., either ‘A’ or ‘a’ is legal). Your program must
read the file, character by character, counting the total number of occurrences of each type of base.
Your program will then output, for each base, what percentage of the DNA sequence consists of that
base. For example, if the input is the sequence: ACGGGTCGAC then the output will be exactly
these five lines of text:
The DNA sequence has 10 bases
• 20.00% of the bases are A
• 30.00% of the bases are C
• 40.00% of the bases are G
• 10.00% of the bases are T
The output must display the percentages with exactly three places to the left of the decimal point
(to allow for 100%). The output must display the percentages with exactly two places to the right of
the decimal point. The percent signs in the output must all be vertically aligned.
If your program successfully completes its task, then the program should return an exit status of
0 to the operating system. The input data file may contain any arbitrary “white space” (tabs, blank
spaces, newlines) intermixed with the characters representing the DNA bases. These chars should not
be counted. If the input data contains any other symbols, then your program should abort processing,
and return an exit status of 1 to the operating system.
Since there are four kinds of bases, this program is a very natural place to use a switch statement.
Your program must incorporate a switch. Your program must read from the standard input (stdin),
and not from any other file.
Create a .c file for this assignment and name it using your last name and the initial of your first
name, like this: lastName initialFirstName DNA.c
To compile your file you should use the command:
$ gcc -std=c99 -pedantic -Wall lastName initialFirstName DNA.c
I have provided four input files and the corresponding correct output files for three of them; one
of the input files has other symbols. If you develop a program called with the requested name for this
assignment, then you can test your program using the first test data file as follows:
$ gcc -std=c99 -pedantic -Wall lastName initialFirstName DNA.c
$ ./a.out < dnaInput 1 > myOutput 1
$ diff myOutput 1 outputFile 1
2
You may repeat this process for all the other dnaInput i files where i may be 2, 3 or 4. The output of
your program should be char-by-char identical to the given outputFile files, for those input files with
correct input. The diff command will display any places where the two argument files are different. If
the diff command is silent, then you know the two files are the same. We will also run your program
with other input to make sure it behaves according to the specifications given in this statement.
If at any time when you are running your program, and you are “stuck” (the program has fallen
into an infinite loop, or is unresponsive) you can “bail out” and halt the execution of the program using
Ctrl + C (i.e., hold Control and C simultaneously).
You should be sure to include THE NAME OF THE AUTHOR OF THE PROGRAM in a
comment at the top of your source code file, for this and all other assignments in this course.
Your source code must use proper style, that is variables should be well named (name is not too
short, not too long, and is meaningful), and bodies of loops, if’s, etc.. should be properly indented.
Refer to the coding style file for this class, published on Canvas under Coding Standards in a file named:
cs241 codingStandards2020.pdf
3 What to submit:
Submit your C program in a file named: lastName InitialFirstName DNA.c
4 Grading rubric:
If your C program does not compile with the -std=c99 -pedantic -Wall options without errors or
warnings the points given for the assignment will be zero. Otherwise the following rubric will be used:
+ 10 pt: Your C files follow the class coding style.
+ 60 pt: Your lastName InitialFirstName DNA.c file passes the diff test using the first three
input files in this assignment.
+ 30 pt: Your lastName InitialFirstName DNA.c file passes diff tests with dnaInput 4 and
other local files available to the graders.
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