Suggested solutions exercises 1-10

1.py
Code

#!/usr/bin/env python3

for i in range(1,1001): # 1001 is exclusive

if i % 3 == 0:
print(i)

2.py
Code

#!/usr/bin/env python3

for i in range(3000,4001): # 4001 is exclusive

if i % 3 == 0:
if i % 5 == 0:
continue
print(i)

1
3.py
Code

#!/usr/bin/env python3

# The number will be imported as a string so we cast it to an integer

userValue = int(input('Type a number: '))

if userValue == 1:
print(1)
elif userValue == 2:
print(1, '\n', 1, sep='')
else:
print(1, '\n', 1, sep='')
values = [1, 1]
for i in range(userValue - 2):
newValue = sum(values)
print(newValue)
values[0] = values[1]
values[1] = newValue

2
4.py
Code

#!/usr/bin/env python3

import sys
number = int(input('Type a number: '))

if number == 0:
print(1) # 0! = 1
sys.exit() # To avoid an else statement
elif number < 0:
print('The number can not be negative', file=sys.stderr)
sys.exit() # To avoid an else statement

total = 1

for i in range(2, number + 1):

total *= i

print(total)

3
5.py
Code

#!/usr/bin/env python3

# https://en.wikipedia.org/wiki/List_of_prime_numbers#The_first_1000_prime_numbers

primeList = ['2'] # Ta be able to join in the last step the list must contain strings
currentValue = 3
while True:

prime = True # We assume that the value we test is a prime

# We only test a factor up to half of the number we investigate to save speed

for i in range(3, int((currentValue + 1) / 2), 2):
# If we find that the number dividable by a smaller number
# it's not a prime and we break
if currentValue % i == 0:
prime = False
break

if prime is True:
# To be able to join in the last step the list must contain strings
primeList.append(str(currentValue))

currentValue += 2 # We only test 3, 5, 7 and so on as the denominators to save speed

if len(primeList) == 1000:
print('\n'.join(primeList))
break

4
6.py
Code

#!/usr/bin/env python3

import re
import sys
import random

nucleotide = ('a', 'c', 'g', 't')

oligo = input('Type a sequence: ')

# Test is the string the user types is valid

matchObject = re.match('[acgtACGT]{' + str(len(oligo)) + '}', oligo)
if not matchObject:
print('Only characters a, c, g, t, A, C, G, T should be used', file = sys.stderr)
sys.exit()

oligoLowercase = oligo.lower() # So we do the comparisons using only lowercase nucleotides

while True: # There is a 25% risk that we pick a nucleotide that the position already has

randomPosition = random.randrange(len(oligo)) # Pick a random position

indexNt = random.randrange(len(nucleotide)) # And the length is of course 4
randomNucleotide = nucleotide[indexNt]

if oligoLowercase[randomPosition] != randomNucleotide:
# The oligo string is immutable so we print out two parts
# that have not changed plus the mutated nucleotide
print(oligoLowercase[:randomPosition] + randomNucleotide + \
oligoLowercase[randomPosition + 1:])
break # When we found a different nucleotide we break the while loop

5
7.py
Code

#!/usr/bin/env python3

ingredients = ['bread']
ingredient1 = input('Input first ingredient: ')
ingredients.append(ingredient1)
ingredient2 = input('Input second ingredient: ')
ingredients.append(ingredient2)
ingredient3 = input('Input third ingredient: ')
ingredients.append(ingredient3)
ingredients.append('bread')

print(ingredients)

6
8.py
Code

#!/usr/bin/env python3

import re
import sys

par = [4, 3, 5, 2, 5, 4, 7, 6]

hole = input('Which hole? ')

# Test is the hole number is valid

matchObject = re.match('[1-8]$', hole) # If we don't use $ the user could input 10
if not matchObject:
print('Only numbers between 1 and 8 can be used', file = sys.stderr)
sys.exit()
hole = int(hole) # Cast from string to integer

strokes = input('How many strokes? ')

# Test is the stroke number is valid

matchObject = re.match('\d+$', strokes)
if not matchObject:
print('Only positive numbers can be used', file = sys.stderr)
sys.exit()
strokes = int(strokes) # Cast from string to integer

result = strokes - par[hole - 1] # -1 to get the index right

if result <= -3:

print('Albatross')
elif result == -2:
print('Eagle')
elif result == -1:
print('Birdie')
elif result == 0:
print('Par')
elif result == 1:
print('Boogie')
elif result >= 2:
print('Double boogie')

7
9.py
Code

#!/usr/bin/env python3

import sys
import os.path

if len(sys.argv) != 3:
print('The program should be run as 9.py fasta_file sequence_id', file=sys.stderr)
sys.exit()

if not os.path.isfile(sys.argv[1]):
print("The input file doesn't exist", file=sys.stderr)
sys.exit()

i = 0 # row counter

with open(sys.argv[1]) as fin:

for line in fin:

i += 1
if line.startswith('>'):
id = line.split()[0]
id = id[1:] # Remove the >
if id == sys.argv[2]:
print('The sequence for id {} starts at line {}'.format(id, i +1))

8
10.py
Code

#!/usr/bin/env python3

import sys
import os.path

if len(sys.argv) != 3:
print('The program should be run as 10.py fastq_input_file fasta_output_file', \
file=sys.stderr)
sys.exit()

if not os.path.isfile(sys.argv[1]):
print("The input file doesn't exist", file=sys.stderr)
sys.exit()

i = 0

with open(sys.argv[1], 'r') as fin, open(sys.argv[2], 'w') as fout:

for line in fin:

i += 1
line = line.rstrip()
if i % 4 == 1:
line = line.replace('@', '>', 1) # Only replace first occurance
print(line, file=fout)
elif i % 4 == 2:
print(line, file=fout)