Learning Python Programming Language with Interactive Computing Framework

Som Bohora, Department of Pediatrics

OUHSC, Statistical Computing User Group
Biomedical and Behavioral Methodology Core (BBMC)
Tuesday, March 01, 2016

Outline of presentation

• Python 3 download and installation
  
• Key differences between Python 2 and Python 3
  
• Interactive computing and dynamic reporting with IPython/Jupyter Notebook
  
• Python tutorial
  
  • Why Python?
    
  • Variables, expressions, and statements
    
  • Conditional executions
    
  • Functions
    
  • Iteration
    
  • Standard data types
    
    • Numbers, Strings
      
    • Lists, Tuples, and dictionaries
      
• Files (working with .txt files)
• Compare some python commands with R program
  
• References and resources
  

Python 3 & Jupyter Notebook Installation

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Python overview

• Python is a high-level, general-purpose, interpreted, and object-oriented scripting language
  
• Developed by Guido van Rossum in the late eighties and early nineties in the Netherlands
  
• Derived from many other languages, including C, C++, and other scripting languages
  

• It is copyrighted and is now available under the GNU General Public License (GPL)
  

• No need of type declaration of variables, parameters, functions or methods
  

• Python source files use .py extension and run with command prompt by python filename.py
  
• Python uses 0-based index origin

Python author: Guido van Rossum

Python features

• Easy-to-learn: few keywords,simple structure, and clear syntax.
  
• Easy-to-read: much more clearly defined and visible to the eyes.
  
• Easy-to-maintain: source code is fairly easy-to-maintain.
  
• A broad standard library: very portable and cross-platform compatible
  
• Interactive Mode
  
• Portable: run and interface on a wide variety of platforms
  
• Extendable: one can add low-level modules to the Python interpreter for efficiency.
  
• Databases: provides interfaces to all major commercial databases.
  
• Scalable: provides a better structure and support for large programs than shell.

Why Python?

• A great experience on Day 1 (minimal set up, shallow learning curve, written in plain English, Errors appear on runtime)
  
• Ability to program on the web
  
• Ability to program desktop applications
  
• Increasing use in data science
  
• Marketable professional skills
  
• Community support
  
• It can be easily integrated with C, C++, Java, and other languages

Python IDE

PyDev with Eclipse, Komodo, Emacs, Vim, TextMate, Gedit, python IDLE, NotePad++, PyCharm

Key differences in Python 2.x and 3.x

Parameters	Python 2.x	Python 3.x
print	print 'hello'	print('hello')
integer division	print '3//2=', 3/2	print('3//2=', 1)
xrange	xrange	range
user input	raw_input	input
iterable objects type	list	range

NOTE:

Use `from __future__ import division` within 2.x to do `3.x` way

Variables, expressions and statements

# This is a comment

print('Hello World')

print(type("string"))

# `=` is an assignment statement
def findType(a):
    return type(a)

x, y, z = 1, 3.1415, 'python'
list(map(findType, (x,y,z)))

Hello World
<class 'str'>

[int, float, str]

# Variable names -- Python is case-sensitive
# 76value = 'big parade'
# more@ = 100
# class = 'Biostat'

import keyword 
# print(keyword.kwlist)

Contd variables, expressions and statements

x=5 ; print(x+7)

print(x % 2) # % modulus operator

first = 10 ; second = 15 ; print( first+second )
firstString = str( first ); secondString = str( second )
print( type( firstString ) )
print(firstString + secondString)

# User input 
whatCourse = input("what course is this?\n")  # "\n" is newline character
print(whatCourse)

12
1
25
<class 'str'>
1015
what course is this?
biostat I
biostat I

Conditional execution

Boolean expressions

print(5 == 5) ; print(5 == 6) ; type(True)

True
False

bool

Comparison operators

x = 5; y = 6; x != y; x > y; x >= y; 

x is y; x is not y

True

Logical operators

x > 0 and x < 10
print(not (x > y))   # Is x not greater than y?
x%2 == 0 or  x%3 == 0
17 and True          # any non-zero number is treated as `True`

5%2

True

1

Conditional execution contd

Conditional execution

# x = -1; y =6
if x < 0:
    print("x is positive")
else:
    pass

if x < y:
    print(x, "is less than", y)
elif x > y :
    print(x, "is greater than", y)
else:
    print("x and y are equal")

5 is less than 6

Standard data types

Numbers and Strings

Lists

• A list is a sequence with elements or items of any type seprated by commas
• [] or list() is used to create lists
• Lists are mutable

Data types contd

import math
lst = [2,3,4,1, 'spam', 3.24, math.pi]; print(x)

listWithinList = ['hello', 2.0, 3, [3,6,5]]

empty = []
print(lst, listWithinList, empty)

[2, 3, 4, 1, 'spam', 3.24, 3.141592653589793]
[2, 3, 4, 1, 'spam', 3.24, 3.141592653589793] ['hello', 2.0, 3, [3, 6, 5]] []

# Lists are mutable
listWithinList[0] = "Hi Som"; print(listWithinList)

# `in` operator
"Hi Som" in listWithinList

# looping through a list
for i in lst:
    print(i)

['Hi Som', 2.0, 3, [3, 6, 5]]
2
3
4
1
spam
3.24
3.141592653589793

Data types contd

# Traversing a list
numbers = [3,5,2]
for i in range(len(numbers)):
    numbers[i] = numbers[i] * 2
print(numbers)

[6, 10, 4]

# List operations
a = [1,2,3,5,4,[2,5,1]]; b = [4,5,9]
print(a + b)

print([0]*4)

[1, 2, 3, 5, 4, [2, 5, 1], 4, 5, 9]
[0, 0, 0, 0]

Data types contd

# List slices
print(a[:])
print(a[:3])  # non-inclusive end-point, this gives 0,1,2 elements
print(a[2:])

a[1:3] = [777, 999];  print(a)

# Slice a list within a list
print(a[5][1])

# List methods
c = a[:4]
c.append(888); print(c)
# c.insert(2, 2222222); print(c)  # select a index where you want to insert

# sort lists
c.sort(reverse=True); print(c)
sorted(c, reverse=True)

[1, 777, 999, 5, 4, [2, 5, 1]]
[1, 777, 999]
[999, 5, 4, [2, 5, 1]]
[1, 777, 999, 5, 4, [2, 5, 1]]
5
[1, 777, 999, 5, 888]
[999, 888, 777, 5, 1]
[999, 777, 5, 1]
[777, 5, 1]
3
777
783
['P', 'y', 't', 'h', 'o', 'n', ' ', 'i', 's', ' ', 'a', ' ', 'm', 'a', 'g', 'i', 'c']
['Python', 'is', 'a', 'magic']
Python is a magic

Data types contd

# Delete elements
del c[1]; print(c)       # del c[1:3] for multiple elements
c.remove(999); print(c)

# List and functions
print(len(c)); print(max(c)); print(sum(c))

# Lists and strings
s = 'Python is a magical'
t = list(s); print(t)
split_str = s.split() ; print(split_str); # default separator is ' '

delimiter = ' '
print(delimiter.join(split_str))

Tuples

• A tuple is a sequence of values like list that stores any type of any types separated by commas
• () or tuple() may be used to create lists
• Lists are immutable

Tuples contd

t = ('a', 'b', 'c', 'd','e')  # t = 'a', 'b', 'c', 'd', 'e'  
#  tuple() Although it is not necessary, it is common to enclose tuples in parentheses to

# To create a tuple with a single element
t2 = ('a',)  # t2 = ('a') is  a string

t3 = tuple()
print(t[1:])

# t[0] = 'A'          # Cannot modify it

# You cannot modify the elements of a tuple, but you can replace one tuple with another
t4 = ('A',) + t[1:]
print(t4)

t = tuple('Hello'); print(t)

# Clever application of tuple is: Swap values between two variables
a = 2; b = 3
a, b = b, a

('a', 'b', 'c', 'd', 'e')
('b', 'c', 'd', 'e')
('A', 'b', 'c', 'd', 'e')
('H', 'e', 'l', 'l', 'o')

Tuples contd

# Comparing tuples
print((0, 1, 2) < (0, 3, 4))
print((0, 1, 2000000) < (0, 3, 4))

# Tuple assignment
m = [ 'have', 'fun' ]
x,y = m
(x, y) = m
print(x,y)

True
True
have fun

Dictionaries

• A dictionary is like a list (index position is integer), but more general (indices can be any type)
• Think of it being as mapping between set of indices (keys) and a set of values (key-value pair)
• It is similar to loop up table or associative array or hash table
• {} or dict() is used to create lists
• Dictionaries are mutable
• Duplicate keys are not allowed
• Duplicate values are just fine

Dictionaries contd

# Create a dictionary
eng2sp = dict()

# Add an item to dictionary
eng2sp['one'] = 'uno'

eng2sp = {'one':'uno', 'two':'dos', 'three':'tres'}

# Add an item in dictionary
eng2sp['four'] = 'cuatro'

# Delete item from dictionary
del eng2sp['four'] ; print(eng2sp)

print(eng2sp['two']); print(len(eng2sp))

print('one' in eng2sp)  # default loop up is `keys`

# To see whether something appears as value
print('uno' in eng2sp.values())

{'three': 'tres', 'one': 'uno', 'two': 'dos'}
dos
3
True
True

Dictionaries contd

# Looping through dictionaries
for key,value in eng2sp.items():
    print(key, value)

vals1 =eng2sp.keys()       # Similarly .value() gives values
# g = list(vals1) # change to list
print(vals1)

# Another dictinary example
d = {'a':10, 'b':1, 'c':22}
t =d.items(); print(t) ; print(sorted(t))   # items() returns a list of tuples

for key in d:
    if d[key] > 10:
        print(key, d[key])

# sort by value
l = list()
for key, value in d.items():
    l.append( (value, key) )
    l.sort(reverse=True)
print(l)

# changing value of an element of a list
x = [5, None, 10] ; print(x)
for idx, i in enumerate(x):
    if i == 5:
        x[idx] =1000
print(x)

seasons = ['Spring', "Summer", "Fall", "Winter"]
list(enumerate(seasons))

three tres
one uno
two dos
dict_keys(['three', 'one', 'two'])
dict_items([('c', 22), ('a', 10), ('b', 1)])
[('a', 10), ('b', 1), ('c', 22)]
c 22
[(22, 'c'), (10, 'a'), (1, 'b')]
[5, None, 10]
[1000, None, 10]

[(0, 'Spring'), (1, 'Summer'), (2, 'Fall'), (3, 'Winter')]

Functions

try and except

def divide(a,b):
    try:
        return True, a/b
    except:
        return "Non divisible", None
divide(2,0)

# Writing a function
def addTwo(a,b):
    added = a + b
    return added
print(addTwo(2,3))

5

Functions contd

Built-in and new functions

text = "Hello world"
print(max(text)); print(min(text)) ;len(text)

# Adding new functions
def print_lines():
    print("Hi, I am Som.")
print_lines()

def repeat_lines():
    print("Here begins new function")
    print_lines(); print_lines()
repeat_lines()

w
 
Hi, I am Som.
Here begins new function
Hi, I am Som.
Hi, I am Som.

Iteration

x = 0
x = x + 1; print(x)

# For loops
for i in range(4):      # end is non-inclusive
    print("The value is:", i)
print("Done")

for letter in "python":
    print("The letter is,", letter)

friends = ['Binod', 'Achyut', 'Bikram']
for friend in friends:
    print(friend, 'has', len(friend), 'letters.')
    
for i in range(0,2):
    for j in "Hi":
        print(i,j)

1
The value is: 0
The value is: 1
The value is: 2
The value is: 3
Done
The letter is, p
The letter is, y
The letter is, t
The letter is, h
The letter is, o
The letter is, n
Binod has 5 letters.
Achyut has 6 letters.
Bikram has 6 letters.
0 H
0 i
1 H
1 i

Iteration contd

# While loops
n = 5
while (n > 0):                 # while n > 0, display, and reduce by 1
    print(n)
    n = n - 1
print('Done')

# Take user input until they type `done`
while True:
    line = input('> ')
    if line[0] == '#':
        continue
    if line == 'done' or line == 'Done':
        break
    print(line)
print('Done')

Strings

• A string is a sequence of characters
• Characters can be accessed one at a time with a bracket operator
• Strings are immutable

Strings contd

# Strings are immutable
fruit = 'apple'   # [0] = 'a', [1] = 'p', [2] = 'p', [3] = 'l',[4] = 'e',
print(fruit[1], len(fruit))
  
length = len(fruit)
# print(fruit[length])   # 0:5, but asking out of range
print(fruit[length-1])

# Traversing through a string
for char in fruit:
    print(char)

# Traversing through a string with index
for idx, val in enumerate(fruit): # getting index of loops
    print(idx, val)
    
# `in` operator
'a' in 'Anaconda'

# String methods
print(type(program))
print(dir(program))

p 5
e
a
p
p
l
e
0 a
1 p
2 p
3 l
4 e
Jytho
 in Ja
Jython in Java
Jyt
hon in Java
Mello friends!
2
<class 'str'>
['__add__', '__class__', '__contains__', '__delattr__', '__dir__', '__doc__', '__eq__', '__format__', '__ge__', '__getattribute__', '__getitem__', '__getnewargs__', '__gt__', '__hash__', '__init__', '__iter__', '__le__', '__len__', '__lt__', '__mod__', '__mul__', '__ne__', '__new__', '__reduce__', '__reduce_ex__', '__repr__', '__rmod__', '__rmul__', '__setattr__', '__sizeof__', '__str__', '__subclasshook__', 'capitalize', 'casefold', 'center', 'count', 'encode', 'endswith', 'expandtabs', 'find', 'format', 'format_map', 'index', 'isalnum', 'isalpha', 'isdecimal', 'isdigit', 'isidentifier', 'islower', 'isnumeric', 'isprintable', 'isspace', 'istitle', 'isupper', 'join', 'ljust', 'lower', 'lstrip', 'maketrans', 'partition', 'replace', 'rfind', 'rindex', 'rjust', 'rpartition', 'rsplit', 'rstrip', 'split', 'splitlines', 'startswith', 'strip', 'swapcase', 'title', 'translate', 'upper', 'zfill']
ANACONDA
2
here we go
False
A
uct.ac.za
There are 99 pythons.
The value of pi i.e. 3.14 can be rounded to 3.

Strings contd

# String slices
s = 'Jython in Java'
print(s[0:5]); print(s[6:12]); print(s[:]); print(s[:3]); print(s[3:])

# Strings are immutable
greeting = 'Hello friends!'

# greeting[0] = 'M'; print(greeting)     # DOES NOT WORK

# Slice and concatenate
new_greeting = 'M' + greeting[1:] ; print(new_greeting)

# Looping and counting
program = 'Anaconda'
count = 0
for letter in program:
    if letter == 'a':
        count += 1
print(count)

Jytho
 in Ja
Jython in Java
Jyt
hon in Java
Mello friends!
2

Strings contd

# Change case
print(program.upper()) ; print(program.find('a'))   # finds first occurence

# remove space at the begining and end of the string 
print('  here we go   '.strip())
print(program.startswith('b'))  # logical
print(program.upper()[program.upper().startswith('A')-1])   #  get the letter
# print(True - 1)

# Parsing the strings
data = 'From stephen.marquard@uct.ac.za Sat Jan  5 09:14:16 2008'
at_position = data.find('@')
space_position = data.find(' ', at_position)
host = data[at_position+1:space_position] ; print(host)

# Format operator `%`
value = 99
print('There are %d pythons.' %value)
print('The value of %s i.e. %g can be rounded to %d.' % ('pi', 3.14, 3))

ANACONDA
2
here we go
False
A
uct.ac.za
There are 99 pythons.
The value of pi i.e. 3.14 can be rounded to 3.

# Making sure that only values greater than are allowed
while True:
    try:
        firstValue = int(input("Enter first number:"))
    except ValueError:
        print()
    else:
        if firstValue > 0:
            break
        else:
            print("ERRORS!!! Please enter value greater than 0")

# Print type of operations
print("Choose operation: 1-add, 2-subtract,3-multiply, 4-divide")

# Storing input type from above list
operation = input("Choose operation from above list (1/2/3/4): ")

# Making sure that only values greater than are allowed
while True:
    try:
        secondValue = int(input("Enter second number:"))
    except ValueError:
        print()
    else:
        if secondValue > 0:
            break
        else:
            print("ERROR!!! Please enter value greater than 0")

# Conditional execution to perform selected tasks of calculation
if operation == '1':
    result = (firstValue + secondValue)
elif operation == '2':
    result = (firstValue - secondValue)
elif operation == '3':
    result = (firstValue * secondValue)
elif operation == '4':
    result = (firstValue / secondValue)
else:
    print("Invalid input")
print(result)
print("Done calculation!!!")
#quit()

Enter first number:2
Choose operation: 1-add, 2-subtract,3-multiply, 4-divide
Choose operation from above list (1/2/3/4): 2
Enter second number:6
-4
Done calculation!!!

Files

• Opening, reading, and searching through .txt files

# reading from a text file

print("Opening file")
text_file = open("test.txt", "r")   # or open("test.txt").read()
print(text_file)
#print(dir(text_file))

#print(text_file.read(1))       # reads first character
#print(text_file.read(5))       # reads fifth character (skips first character as you already read it)

# wholeFile = text_file.read()     # reads whole file (skips already read character)
# print(wholeFile.split())         # splits by space


# print(text_file.readline())    # reads first line
# print(text_file.readline(5))    # reads 4 characters from first line

Opening file
<_io.TextIOWrapper name='test.txt' mode='r' encoding='cp1252'>

Contd Files

lines = text_file.readlines()    # reads all lines and results in  a list with newline character
print(lines)

# for i in lines:     # there is a carriage return ('\n' character)
#     i = i.rstrip()
#     print(i)

# Searching through a file
for line in lines:
    line = line.rstrip()                      # lstrip removes spaces from left
    if not line.startswith("Man"):
        continue   # if line.startswith('From '):
    words = line.split()
    print(line)                                                            

text_file.close()

['I am a test file.\n', 'Maybe someday, he will promote me to a real file.\n', 'Man, I long to be a real file\n', 'and hang out with all my new real file friends.']
Man, I long to be a real file

Python commands the R way

Note: Python base is used and numpy as np is used whenever appropriate

Methods	R	Python 3.x
command line program	r print("hi")	python print("hi")
block delimiters	{ }	offside rule
assignment	i = 3; i <- 3; 3 -> i; assign("i", 3)	i = 3
null	NA or NULL	None or np.nan
null test	is.na(x) or is.null(x)	x == None or x is None
condition expression	if (x > 0) y else -y or ifelse	y if x > 0 else -y
True/False	TRUE FALSE T F	True False
logical operator	&, |, !	and, or, not
integer division	13 %/% 5	13 // 5
paste0	paste("one", "two") = "onetwo"	"one" + "two"
case change	tolower("FOO")	'foo'.upper()
# characters	nchar("hi")	len("hi")
start index	1	0
concatenation	a=c(1,2) ; a2<-append(a,c(2,3))	a + [2,3]
sequence	seq(0,100,10)	range(0,101,10)

Methods	R	Python 3.x
element type	A = array(c(1,2,3))	np.array([1,2,3])
matrix	A = matrix(c(1, 2, 3, 4), nrow=2)	A = np.array([[1, 2], [3, 4]])
dictionary	d=list(n=10, avg=3.6, sd=0.3)	d = {'n': 10, 'avg': 3.6, 'sd': 0.3}
update	d$var = d$sd**2	d['var'] = d['sd']**2
function	add = function(x, y) {x + y}	def add(x,y): x + y
break continue	break next or ifelse	break continue
install package	install.packages("ggplot2")	pip3 install scipy
data type	class	type
undefine variable	rm(x)	del(x)
eval	eval(parse(text='1 + 1'))	eval('1 + 1')
help	help(x) or ?x	help(x)
load package	library("dplyr")	import math

References and resources

• Python documentation http://python.org/
• Books include:
  • Python for Informatics by Charles Severance
  • Learning Python by Mark Lutz
  • Python Essential Reference by David Beazley
  • Python Cookbook, ed. by Martelli, Ravenscroft and Ascher
  • http://wiki.python.org/moin/PythonBooks

Thanks!

Coming up -- Python for Data Science with pandas, numpy, and scikit-learn