Appendix B — Basics: Practice Problem Solutions

B.1 Solution to Problem A.1

species_name = "Escherichia coli"
genome_size = 4_600_000

print(f"The species {species_name} has a genome size of {genome_size} base pairs.")

The species Escherichia coli has a genome size of 4600000 base pairs.

B.2 Solution to Problem A.2

gc_count = 19_123
total_bases = 40_000

gc_content = gc_count / total_bases
print(f"GC content: {gc_content:.2f}")

GC content: 0.48

B.3 Solution to Problem A.3

sequence = "ACTGGTCAA"
print(f"{sequence=}")

first_four = sequence[0:4]
last_five = sequence[4:9]
print(f"{first_four=}; {last_five=}")

combined = first_four + last_five
print(f"{combined=}")

sequence='ACTGGTCAA'
first_four='ACTG'; last_five='GTCAA'
combined='ACTGGTCAA'

B.4 Solution to Problem A.4

quality_score = 28
if quality_score >= 30:
    print("Pass")
else:
    print("Fail")

is_long_enough = True
is_high_quality = False

if is_long_enough and is_high_quality:
    print("Accepted")
else:
    print("Rejected")

Fail
Rejected

B.5 Solution to Problem A.5

expression_levels = [2.1, 3.4, 1.8, 6.2, 4.0]

min_value = min(expression_levels)
max_value = max(expression_levels)
mean_value = sum(expression_levels) / len(expression_levels)


print(f"min: {min_value}")
print(f"max: {max_value}")
print(f"mean: {mean_value}")

first_item = expression_levels[0]
print(f"type of first item: {type(first_item)}")

min: 1.8
max: 6.2
mean: 3.5
type of first item: <class 'float'>

B.6 Solution to Problem A.6

sequences = []

if sequences:
    print("Sequences loaded!")
else:
    print("No sequences found!")

print(bool(""))
print(bool("AGTC"))
print(bool(0))
print(bool(3.14))
print(bool([]))
print(bool(["AGTC"]))

No sequences found!
False
True
False
True
False
True

B.7 Solution to Problem A.7

str = "ACTG"
print(len(str))

# Note: Don't worry about the try/except for now.
# There will be a whole chapter about it later!
try:
    pi = str(3.14)
except TypeError as error:
    print(f"There was an error! {error=}")

4
There was an error! error=TypeError("'str' object is not callable")

B.8 Solution to Problem A.8

read_length = 120
gc_content = 0.55
quality_score = 32

read_length_good = read_length >= 100
gc_content_good = 0.4 <= gc_content <= 0.6
quality_score_good = quality_score > 30

if read_length_good and gc_content_good and quality_score_good:
    print("Read passes all quality filters")
else:
    print("Read filtered out")

Read passes all quality filters

B.9 Solution to Problem A.9

gene_id = "nrdA"
p_value = 0.000012345

print(f"Gene {gene_id} => {p_value:.2e}")

if p_value < 0.01:
    print("Highly significant")
elif p_value < 0.05:
    print("Significant")
elif p_value < 0.10:
    print("Almost significant")
else:
    print("Not significant")

Gene nrdA => 1.23e-05
Highly significant

B.10 Solution to Problem A.10

dna_sequence = "TGacTGatcGT".upper()

sequence_length = len(dna_sequence)

a_count = dna_sequence.count("A")
c_count = dna_sequence.count("C")
g_count = dna_sequence.count("G")
t_count = dna_sequence.count("T")

ambiguous_count = dna_sequence.count("N")

gc_content = (g_count + c_count) / sequence_length * 100

molecular_weight = (
    a_count * 313.2 + t_count * 304.2 + c_count * 289.2 + g_count * 329.2 + 79.0
)

print(f"DNA Sequence: {dna_sequence}")
print(f"Length: {sequence_length}")
print(f"Nucleotide counts")
print(f"A: {a_count}, C: {c_count}, G: {g_count}, T: {t_count}")
print(f"Ambiguous count: {ambiguous_count}")
print(f"GC Content (%): {gc_content:.1f}")
print(f"Molecular weight: {molecular_weight:.1f}")

DNA Sequence: TGACTGATCGT
Length: 11
Nucleotide counts
A: 2, C: 2, G: 3, T: 4
Ambiguous count: 0
GC Content (%): 45.5
Molecular weight: 3488.2

B.11 Solution to Problem A.11

sequence_length = 250
quality_score = 32
ambiguous_bases = 1

if sequence_length >= 200:
    if quality_score >= 30:
        if ambiguous_bases <= 1:
            print("Sequence accepted")
        else:
            print("Sequence rejected: too many ambiguous bases")
    else:
        print("Sequence rejected: low quality")
else:
    print("Sequence rejected: too short")

Sequence accepted

Optional Extension

Here is one way you might solve the optional extension for this problem:

sequence_length = 250
quality_score = 32
ambiguous_bases = 1

if sequence_length < 200:
    print("Sequence rejected: too short")
elif quality_score < 30:
    print("Sequence rejected: low quality")
elif ambiguous_bases > 1:
    print("Sequence rejected: too many ambiguous bases")
else:
    print("Sequence accepted")

Sequence accepted