from scratch
A primer for scientists working with Next-Generation-
Sequencing data
CHAPTER 4
Writing your own functions
Why functions?
Often the same task needs to be performed at different times
in a program.
Copying and pasting lines is error-prone and leads to bloated
code.
Functions enable you to reuse bits of code without the need
of copying it.
What is a function?
We have seen several examples:
● print
● open
● ...
Essentially a function is
● a block of code
● identified and called by a name
Functions can have
● arguments (input values)
● a return value (output)
Defining a function
function name argument
def get_gc_content(dna):
length = len(dna)
g_count = dna.count('G')
c_count = dna.count('C')
gc_content = (g_count + c_count) / length
return gc_content
body: defines code to run and return value
head: defines name and input parameters
Note: This function will not work correctly with Python 2 unless you include the following
import at the top.
from __future__ import division
Calling a function
● functions are called by their defined name:
gc_content = get_gc_content("ATAGGCACATT")
● only when the function is called, its code is executed
● if a return value is returned by the function it can be
assigned to a variable
– if no return statement was defined, the function
returns the value None
Using our function in a program
● a program can comprise several functions and calls to
those functions
● programs are usually considered to be more complex and
structured than scripts, which often only implement a small
subtask
def get_gc_content(dna):
[...]
return gc_content
my_gc_content = get_gc_content("ATGCGCGATCGATCGAATCG")
print(str(my_gc_content))
print(get_gc_content("ATGCATGCAACTGTAGC"))
print(get_gc_content("aactgtagctagctagcagcgta"))
Improving our function
● we can make the output nicer by rounding the return value:
def get_gc_content(dna):
[...]
return round(gc_content, 2)
● Still, the result for the lower case sequence is incorrect.
We can make the script ignore case by formatting the
input parameter:
def get_gc_content(dna):
g_count = dna.upper().count('G')
c_count = dna.upper().count('C')
[...]
Improving our function
● More flexibility can be achieved by making the number of
significant figures an input parameter:
def get_gc_content(dna, ndigits):
length = len(dna)
g_count = dna.upper().count('G')
c_count = dna.upper().count('C')
gc_content = (g_count + c_count) / length
return round(gc_content, ndigits)
Keyword arguments
● A slightly different way of calling a function (or method):
get_gc_content(dna="ATAGGCACATT", ndigits=3)
● identical to the call we used before:
get_gc_content("ATAGGCACATT", 3)
● BUT now we can change the parameter order:
get_gc_content(ndigits=3, dna="ATAGGCACATT")
● Can make calling of functions more descriptive
Parameter defaults
● Some parameters are provided for flexibility but in most cases
a reasonable default value can be assumed
def get_gc_content(dna, ndigits=2):
[...]
return round(gc_content, ndigits)
● Now we can omit the parameter if we are fine with the
default value:
gc_content = get_gc_content("ATAGGCACATT")
● Especially useful for functions with many input parameters
Encapsulation
● putting bits of code that perform a defined subtask into a
function is called encapsulation
● encapsulation enables you to deal with only parts of the
code at a time, a method of abstraction
● well-structured code is much easier to maintain and to
understand
● the whole concept of object-oriented programming is
based on encapsulation
Testing functions
● the assert function is a means of testing a function's
output:
assert get_gc_content("ACGT") == 0.5
assert get_gc_content("acgt") == 0.5
assert get_gc_content("ACT", 3) == 0.333
●
assert returns an exception if the comparison returns
false, otherwise nothing
● for complex programs with many functions it is
good practice to write so-called unit tests to make
sure functions work as expected at all times
● unit tests are usually stored in separate test scripts
Recap
In this unit you learned:
● defining functions
● calling functions
● passing input values to functions as parameters
– defining default values for parameters
– passing parameters by name as keyword arguments
● returning output values from within functions
● testing functions
● the concept of encapsulation
Exercise 4-1: Amino Acid Content (pt. 1)
● Write a function aa_content that takes two arguments:
– a protein sequence
– an amino acid residue code (single letter)
● The function should return the percentage of the protein
that the amino acid makes up.
● Use the following assertions to test your function:
assert aa_content("MSRSLLLRFLLFLLLLPPLP", "M") == 5
assert aa_content("MSRSLLLRFLLFLLLLPPLP", "r") == 10
assert aa_content("MSRSLLLRFLLFLLLLPPLP", "L") == 50
assert aa_content("MSRSLLLRFLLFLLLLPPLP", "Y") == 0
Exercise 4-2: Amino Acid Content (pt. 2)
● Modify the function from part one so that it accepts a list of
amino acid residues rather than a single one.
● If no list is given, the function should return the percentage
of hydrophobic amino acid residues (A, I, L, M, F, W, Y, V).
● Your function should pass the following assertions:
assert aa_content("MSRSLLLRFLLFLLLLPPLP", ['M']) == 5
assert aa_content("MSRSLLLRFLLFLLLLPPLP", ['M','L']) == 55
assert aa_content("MSRSLLLRFLLFLLLLPPLP", ['F','S','L']) == 70
assert aa_content("MSRSLLLRFLLFLLLLPPLP") == 65
