Appendix C — Collections: Practice Problems

Author

Ryan M. Moore, PhD

Published

May 27, 2025

Modified

September 3, 2025

These are the practice problems for Chapter 2. For solutions, see Appendix D.

C.1 Creating and Accessing Lists

Task Description

Create a list called gene_names containing the strings "TP53", "BRCA1", and "MDM2". Then, print out each gene name by accessing its items one at a time using their indices.

Learning Objectives

  • Create a list with multiple items
  • Access list elements by index
  • Print list elements

Solution

# Write your code here!

Test Cases

# Should print:
# TP53
# BRCA1
# MDM2

Common Issues

  • Forgetting to use square brackets for list creation or indexing
  • Starting index at 1 instead of 0

Optional Extensions

  • Use a for loop to print all gene names

C.2 Slicing Lists

Task Description

Given the list bases = ["A", "T", "G", "C", "A", "T"], use slicing to create: - first_three, the first three items, - last_two, the last two items.

Print both variables.

Learning Objectives

  • Use list slicing to extract parts of a list

Solution

# Write your code here!

Test Cases

# Output:
# ['A', 'T', 'G']
# ['G', 'C']

Common Issues

  • Off-by-one errors in slicing
  • Misusing negative indices

Optional Extensions

  • Print the middle two items of the list
  • Practice getting different sized slices from the end of the collection

C.3 Using List Methods: append and remove

Task Description

Start with genes = ["TP53", "BRCA1"]. Add "ATM" to the end of the list, then remove "BRCA1". Print the resulting list.

Learning Objectives

  • Modify lists by adding and removing items
  • Use append() and remove() list methods

Solution

# Write your code here!

Test Cases

# Output:
# ['TP53', 'ATM']

Common Issues

  • Trying to remove an item not present in the list
  • Using list methods as built-in functions (e.g., append(numbers, 3) rather than numbers.append(3))

Optional Extensions

  • Add another gene at the start using insert()

C.4 Creating a Tuple

Task Description

Store the chromosome location for a gene, which starts at position 2_345_678 and ends at 2_346_987, as a tuple. Print the tuple.

Learning Objectives

  • Create and print a tuple to store related information

Solution

# Write your code here!

Test Cases

# Output:
# (2345678, 2346987)

Common Issues

  • Using brackets instead of parentheses

Optional Extensions

  • Print the start and end positions separately by indexing the tuple
  • Try to reassign (change) the first element of the tuple to another value. What happens?

C.5 Dictionary Creation and Value Lookup

Task Description

Create a dictionary named gene_functions mapping the gene "TP53" to "tumor suppression" and "BRCA1" to "DNA repair". Then, use the dictionary to print the function of "TP53".

Learning Objectives

  • Create dictionaries with key-value pairs
  • Access dictionary values using keys

Solution

# Write your code here!

Test Cases

# Output:
# tumor suppression

Common Issues

  • Using parentheses or square brackets instead of curly brackets for dictionary literals
  • Misspelling keys

Optional Extensions

  • Try to print the value for a gene that doesn’t exist. What happens?

C.6 Using Dictionary get Method

Task Description

Use the gene_functions dictionary from the previous task. Retrieve the function for "MDM2" safely using the get method, with a default value of "Unknown". Print the result.

Learning Objectives

  • Use the get() method to safely access dictionary values

Solution

# Write your code here!

Test Cases

# Output:
# Unknown

Common Issues

  • Not exactly an “issue” per se, but, forgetting the default value for get, leading to None
  • Confusing square bracket dictionary access and the get() method

Optional Extensions

  • Add "MDM2": "p53 regulation" to the dictionary, then use get again

C.7 Looping Through a List

Task Description

Given expression = [2.3, 3.1, 1.9], write a for loop that prints each value in the list.

Learning Objectives

  • Use a for loop to iterate over a list

Solution

# Write your code here!

Test Cases

# Output:
# 2.3
# 3.1
# 1.9

Common Issues

  • Forgetting indentation within the loop block
  • Using the wrong variable name inside the loop

Optional Extensions

  • Print the index and value together using enumerate()

C.8 Counting Items with a Loop

Task Description

Given the string sequence = "AAGCTTAA", count how many times "A" appears by looping through the string and incrementing a counter variable. Print the count.

Learning Objectives

  • Use a loop and a counter to count characters

Solution

# Write your code here!

Test Cases

# Output:
# 4

Common Issues

  • Counting every base rather than only the adenines
  • Using base = "A" instead of base == "A"

Optional Extensions

  • Use the string method count() to check your answer

C.9 Filtering a List with a For Loop

Task Description

Given a list genes = ["TP53", "BRCA1", "MDM2", "ATM"], create a new list named genes_with_A containing only gene names that include the letter 'A'. Print this filtered list.

Learning Objectives

  • Use a for loop with a conditional to filter and build a new list

Solution

# Write your code here!

Test Cases

# Output:
# ['BRCA1', 'ATM']

Common Issues

  • Forgetting to initialize the new list before the loop
  • Appending all items, not just those with ‘A’

Optional Extensions

  • Solve the same task using a list comprehension

C.10 Using the in Operator

Task Description

Given a list of gene names genes = ["TP53", "BRCA1", "MDM2"], check if "BRCA1" is present in the list, and print "Found" if it is, or "Not found" otherwise.

Learning Objectives

  • Use the in operator to test list membership

Solution

# Write your code here!

Test Cases

# Output:
# Found

Common Issues

  • Checking the wrong value or casing

Optional Extensions

  • Prompt the user to enter a gene name and check if it’s in the list

C.11 Nested Lists and Indexing

Task Description

Given the nested list:

samples = [
    ["Sample1", [1.1, 1.2, 1.3]],
    ["Sample2", [2.1, 2.2, 2.3]],
    ["Sample3", [3.1, 3.2, 3.3]],
]

Print the value 3.1 by correctly indexing into samples.

Learning Objectives

  • Index into nested lists

Solution

# Write your code here!

Test Cases

# Output:
# 3.1

Common Issues

  • Mixing up list indices
  • Using the 1-based indexing rather than 0-based indexing (especially if you’re used to the R programming language)

Optional Extensions

  • Print all values for “Sample2”
  • Use nested for loops with enumerate to print values with their indices

C.12 Building a Dictionary from Two Lists

Task Description

You are given:

gene_ids = ["nrdA",  "nrdJ", "nrdD"]
products = ["Class I RNR", "Class II RNR", "Class III RNR"]

Build a dictionary mapping each gene id to its product using zip() and a for loop. Print the resulting dictionary.

Learning Objectives

  • Loop through multiple lists
  • Build a dictionary programmatically

Solution

gene_ids = ["nrdA",  "nrdJ", "nrdD"]
products = ["Class I RNR", "Class II RNR", "Class III RNR"]

gene_products = {}
for i in range(len(gene_ids)):
    gene_products[gene_ids[i]] = products[i]

print(gene_products)
{'nrdA': 'Class I RNR', 'nrdJ': 'Class II RNR', 'nrdD': 'Class III RNR'}

Test Cases

# Output:
# {'nrdA': 'Class I RNR', 'nrdJ': 'Class II RNR', 'nrdD': 'Class III RNR'}

Common Issues

  • Mixing up the order of items in the zip
  • Mixing up which list provides keys and which provides values
  • In more complicated problems, overwriting existing dictionary keys
  • Potential problems when zipping lists with different lengths

Optional Extensions

  • Use a for loop, but without using the zip() function to get key-value pairs
  • Use zip(), but don’t use a for loop to build the dictionary

C.13 List Comprehension for Sequence Conversion

Task Description

Given dna = "ATGCTTAC", use a list comprehension to generate a list of its RNA bases (replace every "T" with "U", others stay the same). Print the resulting list.

Learning Objectives

  • Use list comprehensions for transformation
  • Apply conditional logic inside a comprehension

Solution

# Write your code here!

Test Cases

# Output:
# ['A', 'U', 'G', 'C', 'U', 'U', 'A', 'C']

Common Issues

  • Using if base = "T" instead of ==
  • Not understanding the position/order of if and else in the comprehension

Optional Extensions

  • Join the resulting list into a string using join()

C.14 Medium: Counting with defaultdict

Task Description

Given a DNA string sequence = "AAGCGAAGCT", use defaultdict from the collections module to count the occurrences of each base. Print the counts for each base.

Learning Objectives

  • Import and use defaultdict
  • Count frequencies programmatically

Solution

# Write your code here!

Test Cases

# Something like:
# A => 4
# G => 3
# C => 2
# T => 1

Common Issues

  • Forgetting to import defaultdict
  • Not using counts[base] += 1 properly

Optional Extensions

  • Try using a regular dictionary rather than a defaultdict
  • Try using a Counter instead of a defaultdict

C.15 Nested Dictionaries and Access

Task Description

Given the nested dictionary:

gene_info = {
    "nrdA": {"product": "Class I RNR", "location": {"start": 1023, "end": 3268}}
}

Print the start and end position of "nrdA" by accessing nested keys.

Learning Objectives

  • Access values in nested dictionaries

Solution

# Write your code here!

Test Cases

# Output:
# start=1023
# end=3268

Common Issues

  • Misplacing or omitting square brackets
  • Wrong ordering of keys

Optional Extensions

  • Try to print a value for a key that does not exist and observe the error
  • Add another gene to the dictionary, and loop through start positions for all genes

C.16 Reverse Complement DNA Sequence

Task Description

Write code that, given a DNA sequence string (e.g., "AAAACCCGGT"), prints its reverse complement as a string. (A <-> T, C <-> G). Use a dictionary for base pairing and a loop.

Learning Objectives

  • Use dictionaries for mapping
  • Loop through a string in reverse
  • Concatenate strings to build a new sequence

Solution

# Write your code here!

Test Cases

# Input: AAAACCCGGT
# Output: ACCGGGTTTT

# Input: "AGTC"
# Output: "GACT"

Common Issues

  • Incorrect complement dictionary
  • Forgetting to reverse the DNA sequence
  • In more realistic problems, improper handling of ambiguous bases (see IUPAC conventions)

Optional Extensions

  • Write your solution using a list comprehension and the join() method
  • Don’t use a dictionary to store base complement info

C.17 Simulating Random Growth in a List

Task Description

Simulate a population of 10 bacteria, each with starting size 5. On each turn, every bacterium will grow or shrink according to these rules:

  • On even numbered turns (0, 2, 4, …), bacteria with even indices grow by 1 unit, and the other bacteria stay the same
  • On odd numbered turns (1, 3, 5, …), bacteria with even indices stay the same, and the other bacteria shrink by 1

Run the simulation for 10 turns, starting with turn 0. At the start of each turn, print the bacteria list. Finally, when the simulation is over, print the final bacteria list.

Learning Objectives

  • Practice with nested loops
  • Update values in a list
  • Check conditions for breaking loops

Solution

# Write your code here!

Test Cases

# Output:
# Turn 0: [5, 5, 5, ...]
# Turn 1: [...]
# ...
# Turn 9: [...]
# At the end: [...]

Common Issues

  • 0-based indexing issues or forgetting 0 counts as even
  • Mixing up conditional logic
  • Forgetting how the modulo operator (%) works
  • Printing results at the wrong time in the loop (e.g., at the end rather than the start)

Optional Extensions

  • Track and print the average population size at the end of each turn
  • Change the rules to use the random module to make a more interesting simulation