Background Information
HOMEWORK INSTRUCTIONS
Homework #3
DNA Sequencing Problem
Introduction to Python Programming
West Virginia University
Page 1 of 9 Version 4.0
Modified 11/13/2019
Background Information
Deoxyribonucleic acid (DNA) is a molecule that ca
ies the genetic
instructions used in the growth, development, functioning and
eproduction of all known living organisms and many viruses.
The two DNA strands composed of simpler units called
nucleotides. Each nucleotide is composed of one of four nitrogen-
containing nucleobases — cytosine (C), guanine (G), adenine (A),
or thymine (T). During DNA transcription, DNA is divided into two
sections, coding regions (exons) are separated by noncoding regions
(introns).
Problem Statement
In this assignment, students will investigate how to find introns and exons in DNA
sequences.
Instructions
IMPORTANT: Complete the steps below in the order they are given. Completing the
steps out of order may complicate the assignment or result in an inco
ect result.
1. Download and extract the provided Data Files ZIP file into the same directory
as your source code. It contains the following file for use in this assignment:
a. dna.txt – Sample DNA sequence [1].
2. Create a new Python script named lastname_firstname_hw3_dsp.py.
3. At the beginning of your script, insert a comment block containing the following
information:
# Firstname Lastname
# Date
# Computer Science 293B Section YY
# Homework #3: DNA Sequencing Problem
4. We wish to read data from the text file.
a. Create a function named read_data(). It should take the following
parameter:
Parameter Name Type Description
filename String Name of file to read.
Optional parameter with a default value
of dna.txt
HOMEWORK INSTRUCTIONS
Homework #3
DNA Sequencing Problem
Introduction to Python Programming
West Virginia University
Page 2 of 9 Version 4.0
Modified 11/13/2019
. In the body of the read_data() function, perform the following tasks:
i. Use a try/except block to provide e
or handling while performing
file I/O.
(1) In the body of the try block, perform the following tasks:
(a) Read the entire contents of the text file specified by the
filename variable into a list named data.
(2) In the event of an IOE
or exception, perform the following
tasks:
(a) Print “File not found.”.
ii. Return the data variable.
5. We need to calculate the percentage of the DNA sequence that is composed of
A or T nucleotides.
a. Create a function named get_dna_stats(). It should take the following
parameter:
Parameter Name Type Description
dna_strand String DNA sequence to process.
. In the body of the get_dna_stats() function, perform the following
tasks:
i. Return the percentage of characters in the dna_strand variable
that are As and Ts.
You can calculate the A and T nucleotide content using the following
formula:
?????? ?? ? ??????? + ?????? ?? ? ???????
?????ℎ ?? dna_strand
6. We also wish to find the complement of a given DNA sequence.
a. Create a function named get_dna_complement(). It should take the
following parameter:
Parameter Name Type Description
dna_strand String DNA sequence to process.
. In the body of the get_dna_complement() function, perform the following
tasks:
i. Create the following variable:
Variable Name Type Initial Value(s)
dna_complement String “”
HOMEWORK INSTRUCTIONS
Homework #3
DNA Sequencing Problem
Introduction to Python Programming
West Virginia University
Page 3 of 9 Version 4.0
Modified 11/13/2019
ii. Use a loop to iterate through each character in the dna_strand
variable. Each loop iteration must do the following:
(1) Append a new character to the dna_complement variable
ased on the value of the cu
ent iteration’s nucleotide
character:
DNA Nucleotide DNA Complement
A T
T A
G C
C G
iii. Return the dna_complement variable.
7. We want to print the DNA sequence and its complement.
a. Create a function named print_dna(). It should take the following
parameter:
Parameter Name Type Description
dna_strand String DNA sequence to process.
. In the body of the print_dna() function, perform the following tasks :
i. Call dna_complement()and store the result in a variable named
dna_complement. Specify the following parameters:
Parameter Name Value(s)
dna_strand dna_strand
ii. Use a loop to simultaneously iterate through the dna_strand and
dna_complement lists. Each loop iteration must do the following:
(1) Print a statement listing the cu
ent DNA strand value and its
complement.
iii. Iterate through the dna_strand and dna_complement variables
and print the nucleotide and its complement separated by an equal
sign, following this example: “A = T” .
8. We want to determine the co
esponding RNA sequence from a DNA sequence.
a. Create a function named get_rna_sequence(). It should take the
following parameter:
Parameter Name Type Description
dna_strand String DNA sequence to process.
HOMEWORK INSTRUCTIONS
Homework #3
DNA Sequencing Problem
Introduction to Python Programming
West Virginia University
Page 4 of 9 Version 4.0
Modified 11/13/2019
. In the body of the get_rna_sequence() function, perform the following
tasks:
i. Create the following variable:
Variable Name Type Initial Value(s)
na_complement String ""
ii. Use a loop to iterate through each character in the dna_strand
variable. Each loop iteration must do the following:
(1) Append a new character to the rna_complement variable
ased on the value of the cu
ent iteration’s nucleotide
character:
DNA Nucleotide DNA Complement
A U
T A
G C
C G
iii. Return the rna_complement variable.
9. Exons are parts of genes that encode the final RNA sequences [2]. We wish to
extract specific exons from larger DNA sequences.
a. Create a function named extract_exon(). It should take the following
parameter:
Parameter Name Type Description
dna_strand String DNA sequence to process.
start Int Starting position in the DNA sequence.
end Int Ending position in the DNA sequence.
. In the body of the extract_exon() function, perform the following task:
i. Return a string containing the portion of the dna_strand variable
etween the start and end positions, inclusive.
10. We want to calculate what percentage of the DNA sequence is compromised of
a given exon.
a. Create a function named calculate_exon_pctg(). It should take the
following parameter:
Parameter Name Type Description
dna_strand String DNA sequence to process.
exons List Exons to compare.
HOMEWORK INSTRUCTIONS
Homework #3
DNA Sequencing Problem
Introduction to Python Programming
West Virginia University
Page 5 of 9 Version 4.0
Modified 11/13/2019
. In the body of the calculate_exon_pctg() function, perform the
following tasks:
i. Create the following variable:
Variable Name Type Initial Value(s)
exons_length Int 0
ii. Use a loop to iterate through the exons list. Each loop iteration
must do the following:
(1) Add the length of the cu
ent list element to exons_length.
iii. Return the percentage of the dna_strand variable that is
comprised of elements in the exons list.
You can calculate the percentage using the following formula:
?????_?????ℎ
?????ℎ ?? ???_??????
11. We want to format the DNA sequence with exon regions in uppercase letters
and intron (non-exon) regions in lowercase letters.
a. Create a function named format_dna(). It should take the following
parameter:
Parameter Name Type Description
dna_strand String DNA sequence to process.
. In the body of the format_dna() function, perform the following tasks:
i. Return a string derived from the dna_strand variable where
characters in positions 0 to 62 are uppercase, positions 63 to 90 are
lowercase, and positions 91 to the end are uppercase.
12. We need to write results to a file.
a. Create a function named write_results(). It should take the following
parameters:
Parameter Name Type Description
output List List containing output to write to a file.
filename String Name of file to write output to.
. In the body of the write_results() function, perform the following
tasks:
i. Use a try/except block to provide e
or handling while performing
file I/O.
HOMEWORK INSTRUCTIONS
Homework #3
DNA Sequencing Problem
Introduction to Python Programming
West Virginia University
Page 6 of 9 Version 4.0
Modified 11/13/2019
(1) In the body of the try block, perform the following tasks:
(a) Write the contents of the output list to the file specified
y the filename variable, one row per list element.
(2) In the event of an IOE
or exception, perform the following
tasks:
(a) Print “E
or writing file.”.
13. We also wish to create a main function.
a. Create a function named main(). It should take no parameters.
. In the body of the main() function, perform the following tasks:
i. We wish to read a DNA sequence from the provided data file.
Call read_data()and store the result in a variable named
dna_sequence. Specify the following parameter:
Parameter Name Value(s)
filename dna.txt
ii. Create the following variable:
Variable Name Type Initial Value(s)
Output List [] (empty list)
iii. Append “The AT content is get_dna_stats()% of the DNA
sequence.” to the output list.
Call get_dna_stats() and substitute the result where indicated.
Format the percentage as a percentage with 1 decimal place.
Specify the following parameter:
Parameter Name Value(s)
dna_strand dna_sequence
iv. Append “The DNA complement is get_dna_complement().” to the
output list.
Call get_dna_complement() and substitute the result where
indicated. Specify the following parameter:
Parameter Name Value(s)
dna_strand dna_sequence
HOMEWORK INSTRUCTIONS
Homework #3
DNA Sequencing Problem
Introduction to Python Programming
West Virginia University
Page 7 of 9 Version 4.0
Modified 11/13/2019
v. Append “The RNA sequence is get_rna_sequence().” to the
output list.
Call get_rna_sequence() and substitute the result where indicated.
Specify the following parameter:
Parameter Name Value(s)
dna_strand dna_sequence
vi. Call extract_exon() and store the result in a variable named
exon1. Specify the following parameters:
Parameter Name Value(s)
dna_strand dna_sequence
Start 0
End 62
vii. Call extract_exon() and store the result in a variable named