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Python
Comprehension and Generators
Peter Wad Sackett
List comprehension 1
Creating new list with other list as basis
primes = [2, 3, 5, 7]
doubleprimes = [2*x for x in primes]
The same as
doubleprimes = list()
for x in primes:
doubleprimes.append(2*x)
Any expression (the part before the for loop) can be used.
Example: A tab separated line of numbers are read from a file,
convert the numbers from strings to floats.
for line in datafile:
numbers = [float(no) for no in line.split()]
# Do something with the list of numbers
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DTU Bioinformatics, Technical University of Denmark
List comprehension 2
Filtering with comprehension – using if
odd = [no for no in range(20) if no % 2 == 1]
numbers = [1, 3, -5, 7, -9, 2, -3, -1]
positives = [no for no in numbers if no > 0]
Nested for loops in comprehension
Example: Creating all combinations in tuples of two numbers,
where no number is repeated in a combination.
combi = [(x, y) for x in range(10) for y in range(10) if x != y]
Flatten a list of lists (matrix) into a simple list
matrix = [[1, 2, 3], [4, 5, 6], [7, 8, 9]]
flatList = [no for row in matrix for no in row]
A list does not have to form the basis of the comprehension – any
iterable will do, like sets or dicts.
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Set and dict comprehension
It works like list comprehension, just use {} instead of []
Create a set of all codons
nuc = [’A’, ’T’, ’C’, ’G’]
codons = { x+y+z for x in nuc for y in nuc for z in nuc }
Turning a dict inside out
myDict = {'a': 1, 'b': 2, 'c': 3}
reverseDict = {value:key for key, value in myDict.items()}
Result: {1: 'a', 2: 'b', 3: 'c'}
This only works if the values of the dictionary are immutable.
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DTU Bioinformatics, Technical University of Denmark
Generators
Generators are your own defined iterators, like range.
Generators look like functions, but they keep the state of their
variables between calls, and they use yield instead of return. Also
calling them again resumes execution after the yield statement.
Generators deal with possibly memory issue as values are generated in
the fly.
Example: range(10) returns the numbers between 0 and 9, both
inclusive, myrange(10) returns the numbers between 1 and 10.
def myrange(number):
result = 1
while result <= number:
yield result
result += 1
for i in myrange(10):
print(i)
More info: http://www.programiz.com/python-programming/generator
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Example: Generating a random gene sequence
import random
def randomgene(minlength, maxlength):
yield 'ATG'
counter = 2
while counter < maxlength:
codon = random.choice('ATCG') + random.choice('ATCG') +
random.choice('ATCG')
if codon in ['TGA', 'TAG', 'TAA']:
if counter >= minlength:
yield codon
return
else:
yield codon
counter += 1
yield random.choice(['TGA', 'TAG', 'TAA'])
# Finally using it
print(''.join(randomgene(40,50)))
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DTU Bioinformatics, Technical University of Denmark
Example: Generating a random gene sequence, take 2
import random
def randomgene(minlength, maxlength):
if minlength < 2 or minlength > maxlength:
raise ValueError(’Wrong minlength and/or maxlength')
yield 'ATG'
stopcodons = ('TGA', 'TAG', 'TAA')
countdown = random.randrange(minlength, maxlength+1) - 2
while countdown > 0:
codon = random.choice('ATCG') + random.choice('ATCG') +
random.choice('ATCG')
if codon not in stopcodons:
yield codon
countdown -= 1
yield random.choice(stopcodons)
# Finally using it
print(''.join(randomgene(40,50)))
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DTU Bioinformatics, Technical University of Denmark
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