> For the complete documentation index, see [llms.txt](https://igb.mit.edu/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://igb.mit.edu/mini-courses/python/introduction-to-python-for-biologists/functions.md).
# 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.
