Functions

Functions are like machines

• Learning to write your own functions will greatly increase the complexity of the programs that you can write

• A function is a black box-it takes some input,does something with it, and spits out some output

• Functions hide details away, allowing you to solve problems at a higher level without getting bogged down

Examples

• A typical function looks like this:

def function_name(function_arguments)
   """optional string decribing the function"""
   statements ...
   return result

• A function example: sum

In [1]: numbers=[1,2,3,4,5]

In [2]: sum(numbers)
Out[2]: 15

• Anatomy of sum function

1.initialize the sum to zero
2.loop over each number while adding the number to the sum variable
3.return the value of sum

def sum(xs):
   """Given a sequence of numbers, return the sum."""
   s=0
   for x in xs:
      s=s+x
   return s

• Writing your own function

Open a text editor, type the following and save it as MyMathFunctions.py:
def mysum(numbers):
        """Given a sequence of numbers, return the sum"""
        s=0
        for x in range(numbers):
                s=s+x
        return s

def myproduct(numbers):
        """Given a sequence of numbers, return the product"""
        p=1
        for x in range(numbers):
                p=p*x
        return p

• Importing a function from a file (module)

  • Once we import MyMathFunctions module we just wrote, we can use the mysum function and myproduct function just like the built-in function

  • The way to call a function is to give the function name followed by parenthesis with values for the number of arguments expected

In [1]: import MyMathFunctions

In [2]: numbers=[1,2,3,4]

In [3]: MyMathFunctions.mysum(numbers)
Out[3]: 10

In [4]: MyMathFunctions.myproduct(numbers)
Out[4]: 24

Too many typing strokes? Try the following:

In [5]: import MyMathFunctions as f

In [6]: f.mysum(numbers)
Out[6]: 10

Still too many typing strokes? Try the following:
In [7]: import MyMathFunctions

In [8]: a=MyMathFunctions.mysum

In [9]: a(numbers)
Out[9]: 10

• Function arguments

  • We can define functions with more than one arguments

Example: restrcition.py
def finder(DNA,enzyme):
        db={}
        name=['ECOR1','BAMH1','HINDIII']
        site=['GAATTC','GGATCC','AAGCTT']
        db=dict(zip(name,site))
        DNA=DNA.upper()
        enzyme=enzyme.upper()
        index=DNA.find(db[enzyme])
        if (index>-1):
                print ("The restriction site starts at base pair %d\n" %index)
        else:
                print ("No such restriction site\n")

In [1]: import restriction
In [2]: restriction.finder('ATGGAATTCCGT','EcoR1')
The restriction site starts at base pair 3

In [3]: restriction.finder('ATGGAATTCCGT','BamH1')
No such restriction site

• Arguments with default values do not need to be supplied when calling a function. But if provided, will overwrite the default values

Example: restrcition_BamH1_default.py
def finder(DNA,enzyme='BamH1'):
        db={}
        name=['ECOR1','BAMH1','HINDIII']
        site=['GAATTC','GGATCC','AAGCTT']
        db=dict(zip(name,site))
        DNA=DNA.upper()
        enzyme=enzyme.upper()
        index=DNA.find(db[enzyme])
        if (index>-1):
                print ("The restriction site starts at base pair %d" %index)
        else:
                print ("No such restriction site\n")

In [1]: import restriction_BamH1_default

In [2]: restriction_BamH1_default.finder('ATGGAATTCCGT')
No such restriction site


In [3]: restriction_BamH1_default.finder('ATGGAATTCCGT','Ecor1')
The restriction site starts at base pair 3

• Some existing Python modules

  • The os module provides a platform independent way to work with the operating system, make or remove files and directories

  • The csv module provides readers and writers for comma separated value data

  • The sys module contains many objects and functions for dealing with how python was complied or called when executed

  • The glob module proves the glob function to perform file globbing similar to what the unix shell provides

  • The math module provides common algebra and trigonometric function along with several math constants

  • The re module provides access to powerful regular expression

  • The datetime module provides time and datetime objects. allowing easy comparison of times and dates

  • The time module provides simple estimates for how long a command takes

  • The pickle module provides a way to save python objects to a file that you can unpickle later in a different program

  • The pypi module helps package installation

  • The numpy module is the de facto standard for numerical computing

  • The pandas module is useful for tabular data managing

  • The matplotlib module is the most frequently used plotting package in Python

  • The seaborn module is a module based on matplotlib. It provides a high-level interface for drawing attractive graphics.