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from IPython.display import Image
from IPython.display import clear_output
from IPython.display import FileLink, FileLinks

Introduction to¶

with Application to Bioinformatics¶

- Day 4¶

TODAY¶

Loops and functions
Using somebody else's code (using modules)

Review¶

Why does it matter what type a variable has?
How (and when) can you change the type of those? When does it not work?
You have worked with a number of data containers; lists, sets, dictionaries. What is the difference between them and when should you use which?
What is a function?

Review¶

Why does it matter what type a variable has?

Values of different types stores different types of information.

Different types can be used with different operations, functions and methods.

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1+2

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"1"+"2"

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"1"+2

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"1"*2

Take extra care when comparing values

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2<12

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"2"<"12"

Review¶

How can you change (convert) the type of a value? When does it not work?

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float("1")

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int("1")

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str(1)

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int("2.2")

Converting between strings and lists

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list("hello")

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str(['h', 'e', 'l', 'l', 'o'])

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''.join(['h', 'e', 'l', 'l', 'o'])

Review¶

You have worked with a number of data containers; lists, sets, dictionaries. What is the difference between them and when should you use which?

lists: when order is important
dictionaries: to keep track of the relation between keys and values
sets: to check for membership. No order, no duplicates.

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mylist = ["comedy", "drama", "drama", "sci-fi"]
mydict = {"genre": "drama", "title": "Toy Story"}
myset = set(mylist)
print('All genres', myset)

Review¶

What is a function?

A named piece of code that performs a specific task.

A relation between input data (parameters) and a result (output data).

Function structure¶

The def keyword

Arguments

Indentation!

return

Scope

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def myfunc(a, b):
    print(a)
    
a

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a = 5

def myfunc(a):
    a += 2
    return a
    
b = myfunc(8)

a, b

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a = 3
print('Globally, a is', a)

def myfunc(a):
    print('In f, a is', a)
    a += 2
    print('Then a in f is', a)
    return a
    
print('Calling f with argument 8')
b = myfunc(8)
print('Result of f(8) =', b)
print('Finally the global a is', a)

The local a in myfunc shadows the global a.

The variables inside functions are local. To avoid confusion, use different variable names.

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global_a = 3

def myfunc(value):
    value += 2
    return value
    
result = myfunc(8)

global_a, result

No confusion!

myfunc has unique variable names.

More on functions, loops...¶

Controlling loops - break

for x in lines_in_a_big_file:
    if x.startswith('>'):  # this is the only line I want!
        do_something(x)

...waste of time!

for x in lines_in_a_big_file:
    if x.startswith('>'):  # this is the only line I want!
        do_something(x)
        break  # break the loop

break

Controlling loops - continue

for x in lines_in_a_big_file:
    if x.startswith('>'):  # this is a comment
        # just skip this! don't do anything
    do_something(x)

for x in lines_in_a_big_file:
    if x.startswith('>'):  # this is a comment
        continue  # go on to the next iteration
    do_something(x)

for x in lines_in_a_big_file:
    if not x.startswith('>'):  # this is *not* a comment
        do_something(x)

continue

Another control statement: pass - the placeholder

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def a_function():
    # I have not implemented this just yet

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def a_function():
    # I have not implemented this just yet
    pass

a_function()

Returning nothing

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def a_function():
    pass

def b_function():
    return

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result_a = a_function()
result_b = b_function()
print('a:', result_a, 'b:', result_b)

Another keyword: `None`¶

Other keywords: True, import, and

What is None? What type? Why? When is it used?

What is it?
- A keyword with a constant value (like True, False)

Why and when?
- To signal "emtpy values"
- Functions that don't return anything meaningful
- Variables with no values yet

`None`¶

What type?
- The NoneType

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type(None)

Comparing `None`¶

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None == True

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None == False

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value = None
if value:
    print('value is something')
else:
    print('no value!')

Comparing `None`¶

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None <= 0 

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myvalue = None
if myvalue and myvalue <= 0:
    print('The value is smaller than or equal to 0')
else:
    print('The value is either None or greater to zero')

Keyword arguments

open('../files/250.imdb', 'r', encoding='utf-8')

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def prettyprinter(name, value, delim=":"):
    out = "The " + name + " is " + delim + " " + value + "."
    return out

Programmer can set default values

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prettyprinter("title", "Movie")

User can ignore the arguments (default value is used)

def prettyprinter(name, value, delim=":"):
    out = "The " + name + " is " + delim + " " + value + "."
    return out

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  prettyprinter("genre", "Drama", "=")

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prettyprinter("genre", "Drama", delim="=")

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def prettyprinter(name, value, delim=":", end=None):
    out = "The " + name + " is " + delim + " " + value
    if end:
        out += end
    return out

my_str = prettyprinter("title", "Movie")
print(my_str)

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prettyprinter("genre", "Drama", "=", ".")

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prettyprinter("genre", "Drama", delim="=", end="!")

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prettyprinter("genre", "Drama", end="!", delim=":::")

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prettyprinter("genre", "Drama", end="!")

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prettyprinter("genre", "Drama", delim="=", ".")

Positional arguments comes first, keyword arguments after!

open(file, mode='r', buffering=-1, encoding=None, errors=None,
     newline=None, closefd=True, opener=None)

Gives better overview

open('../files/250.imdb', 'r', encoding='utf-8')

open('../files/250.imdb', mode='r', encoding='utf-8')

open('../files/250.imdb', encoding='utf-8', mode='r')

Keyword arguments¶

programmer: set default values
user: ignore arguments
better overview

Exercise 1¶

→ Notebook Day_4_Exercise_1 (~30 minutes)

Modules¶

Use a module
Create a module

What is a module?¶

a python file

a organizational unit

a library

Remember?¶

Why functions?¶

Cleaner code
Better defined tasks in code
Re-usability
Better structure

Why modules?¶

Cleaner code
Better defined tasks in code
Re-usability
Better structure

Collect all related functions in one file
Import a module to use its functions
Only need to understand what the functions do, not how

Example: sys¶

import sys

sys.argv[1]

Python standard modules¶

Check out the module index

How to find the right module?

How to understand it?

How to find the right module?

look at the module index
search PyPI
ask your colleagues
search the web!

How to understand it?

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import math

help(math)

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dir(math)

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help(math.sqrt)

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 math.sqrt(3)

Different ways of importing¶

Standard:

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import math

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math.sqrt(3)

Alias:

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import math as m

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m.sqrt(3)

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import math as c

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counter = c.Counter()

Get access to only one function:

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from math import sqrt, ceil

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sqrt(3)

When?¶

import math: standard
import xml.etree.ElementTree as ET: for long names
from collections import defaultdict: import only one function/class

Exercise¶

→ Notebook Day_4_Exercise_2 (~30 minutes)

Documentation and commenting your code¶

Remember help()?

Works because somebody else has documented their code!

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def process_file(filename, chrom, pos):
    for line in open(filename):
        if not line.startswith('#'):
            columns = line.split('\t')
            if col[0] == chrom and col[1] == pos:
                print(line)

?

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def process_file(filename, chrom, pos):
    """
    Reads a vcf file and prints the genotype of the samples
    at chromosome chrom and position pos.
    """
    for line in open(filename):
        if not line.startswith('#'):
            columns = line.split('\t')
            if col[0] == chrom and col[1] == pos:
                print(line)

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help(process_file)

Your code may have two types of users:

library users
maintainers (maybe yourself!)

Write documentation for both of them!

library users:""" What does this function do? """ (doc strings)
maintainers: # implementation details (comments)

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def process_file(filename, chrom, pos):
    """
    Reads a vcf file and prints the genotypes of corresponding to
    chromosome chrom and position pos.
    """
    for line in open(filename):
        if not line.startswith('#'):  # skip comments
            columns = line.split('\t')  # file is tab separated
            # Check if chrom and pos match
            if col[0] == chrom and col[1] == pos:
                # genotype starts at column index 9
                print(col[9:])

Your own code as a module¶

Put your code in a file
Document it
Write a main function?

Documentation:¶

At the beginning of the file

""" This module provides functions for..."""

For every function

def make_list(x):    
     """ Returns an list of lenght x """

Comments:¶

Wherever the code is hard to understand

my_list[5] += other_list[3]  # explain why you do this!```

Using your module¶

Save your code in mymodule.py
Run it: python3 mymodule.py
Import it: >>> import mymodule

The main function¶

def main(input_str):
    # do something
    pass

# at the end of the file
if __name__ == "__main__":
   result = main(sys.argv[1])        # get input from command line
   print("The result is: ", result)  # show result to user

When the module is run a a script: read input, print output
When the module is imported: get access to main()

The main function¶

In file module.py:

print("My name is " + __name__)

if __name__ == "__main__":
    print("I'm run as a main module")

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import module as m

But if we run the file module.py as a script:

Summary¶

→ Notebook Day_4_Exercise_3 (~30 minutes)

Using somebody else's code¶

Written by last year's teacher, Frédéric Haziza (slightly modified).

Lets you work with a database with information about real estate around Uppsala.

Have a look at the documentation and the the code!

A lot of new things!¶

classes

class HomeEntry():
    def __init__(self, row):

methods

return self.raw_query(q)

javascript!

function createPopup(feature) {
     feature.popup = new OpenLayers.Popup.FramedCloud("pop",
     ...

...

You don't need to understand these things, as long as you can understand the documentation!

The database¶

A house:
- a HomeEntry
- id, type, location, adress, date, asked_price, price, rooms, area, rent, latitude, longitude

What you need
- latitude, longitude, price, area
- home.get_price(), home.get_location(), home.get_area()

Getting houses from the database¶

database = HomeDB('uppsala.sqlite')
database.connect()```

homes = db.select()  # Get everything```

homes = db.select('price > 1000000')  # Select by some criteria```

homes = db.select('id = "2447"')
    ```

The magic - printing maps¶

plot() creates a html file, which you can open in a browser.

plot(selection,                    # a list of homes to print
     output='selection.html',      # the name of the output file
     special=None,                 # a very special house
     zoom=12,                      # the zoom levl
     latitude=59.83732598851705,   # the center position (lat(
     longitude=17.64549846959149,  # the center position (long)
     radius=5000)                  # circle radius
     ```

selection
output
special

Your program¶

get a collection of houses
sort and organize them
plot them

Other useful functions

haversine()
sort_by_price()

Exercise 4¶

→ Notebook Day_4_Exercise_4 (~60 minutes)

Sum-up day 4¶

control statements: break, continue, pass

None

scope: global and local. Be careful with your variable names!

keyword arguments: open(filename, encoding="utf-8")

Sum-up day 4¶

importing: Python standard modules, your own modules...

documentation: help(), """Doc string""", # comment

main function: what is run when

Introduction to¶

with Application to Bioinformatics¶

- Day 4¶

TODAY¶

Review¶

Review¶

Review¶

Review¶

Review¶

Function structure¶

More on functions, loops...¶

Another keyword: None¶

None¶

Comparing None¶

Comparing None¶

Keyword arguments¶

Exercise 1¶

Modules¶

What is a module?¶

Remember?¶

Why functions?¶

Why modules?¶

Example: sys¶

Python standard modules¶

Different ways of importing¶

When?¶

Exercise¶

Documentation and commenting your code¶

Read more:¶

Your own code as a module¶

Documentation:¶

Comments:¶

Using your module¶

The main function¶

The main function¶

Summary¶

Using somebody else's code¶

A lot of new things!¶

The database¶

Getting houses from the database¶

The magic - printing maps¶

Your program¶

Exercise 4¶

Sum-up day 4¶

Sum-up day 4¶

Another keyword: `None`¶

`None`¶

Comparing `None`¶

Comparing `None`¶