An Introduction to Python – Part II

Dr. Nancy Warter-Perez

Introduction to Python – Part II 2

Overview Data Organization

Lists Tuples Dictionaries

Input/Output Programming Workshop #1 If tests Loops

for while

Example amino acid search program Programming Workshop #2

Introduction to Python – Part II 3

Enclosed in single or double quotesEx: ‘Hello!’ , “Hello!”, “3.5”, “a”, ‘a’

Sequence of characters:mystring=“hello world!”

mystring[0] -> “h” mystring[1] -> “e”

mystring[2] -> “l” mystring[-1] -> “!”

Strings

-1 is last,

-2 next to last, etc…

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String operations

mystring = “Hello World!”

Expression Value Purposelen(mystring) 12 number of characters in

mystring

“hello”+“world” “helloworld” Concatenate strings

“%s world”%“hello” “hello world” Format strings (like sprintf)

“world” == “hello”

“world” == “world”

0 or False

1 or True

Test for equality

“a” < “b”

“b” < “a”

1 or True

0 or False

Alphabetical ordering

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Strings (2) slicing:mystring = “spoon!”

mystring[2:] -> “oon!”mystring[:3] -> “spo” #note last element is never included!

mystring[1:3]-> “po” Many useful built-in functions

mystring.upper() -> “SPOON!” mystring.replace(‘o’, ‘O’) -> “spOOn!”

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Strings (3) “%” operator:

sort of “fill in the blanks” operation:mystring=“%s has %d marbles” % (“John”,35)

mystring -> “John has 35 marbles”

%s replace with string %d,%i replace with integer %f replace with float

Values to put in blanks

“blanks”

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Lists

mylist=[“a”,”b”,3.58,”d”,4,0]mylist[0]mylist[2]

a3.58

Indexing

mylist[-1]mylist[-2]

04

Negative indexing (counts from end)

mylist[1:4] [“b”,3.58,”d”] Slicing (like strings)

“b” in mylist“e” not in mylist

1 or True1 or True

mylist.append(8) [“a”,”b”,3.58,”d”,4,0,8]

Add to end of list

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Tuples Tuples – sequence of values

like lists, but cannot be changed after it is createdmytuple=(1,”a”,”bc”,3,87.2)mytuple[2] -> “bc”

mytuple[1]=“3” Used when you want to pass several

variables around at once

Error!

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Dictionaries Dictionaries – map ‘keys’ to ‘values’

like lists, but indices can be of any type Also, keys are in no particular order Eg:mydict={‘b’:3, ’a’:4, 75:2.85}mydict[‘b’] -> 3mydict[75] -> 2.85mydict[‘a’] -> 4

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Dictionaries

mydict={“r”:1,”g”:2,”y”:3.5,8.5:8,9:”nine”}mydict.keys() ['y', 8.5, 'r', 'g', 9] List of the keys

mydict.values() [3.5, 8, 1, 2, 'nine'] List of the values

mydict[“y”] 3.5 Value lookup

mydict.has_key(“r”) True or 1 Check for keys

mydict.update({“a”:75})

{8.5: 8, 'a': 75, 'r': 1, 'g': 2, 'y': 3.5, 9: 'nine'}

Add pairs to dictionary

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Dictionaries – other considerations Slicing not allowed Referencing invalid key is an error:>>> mydict={8.5: 8, 'a': 75, 'r': 1, 'g': 2, 'y':

3.5, 9: 'nine'}>>> mydict["red"]Traceback (most recent call last):

File "<interactive input>", line 1, in ?KeyError: 'red‘

Use mydict.get(“red”) instead, it returns None if key is not found

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Input/Output Function raw_input() designed to read a line of

input from the user 1 optional argument: string to prompt user If int or float desired, simply convert string:

int(mystring)->convert to int (if possible)

float(mystring)->convert to float (if possible)

>>> mystr=raw_input("Enter a string:")Enter a string:Hello World!>>> mystr'Hello World!'

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Output Function print

Prints each argument, followed by space

After all arguments, prints newline

Put comma after last arg to prevent newline

“add” strings to avoid spaces

print “a”,”b”,”c”a b c

print “a”,”b”,”c”,a b c

print “a”+”b”+”c”abc

Newline!

No Newline!

No spaces!

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Output Example>>> print "hello","world";print "hello","again"

hello world

hello again

>>> print "hello","world",;print "hello","again"

hello world hello again

>>> print "hello %s world" % "cold and cruel"

hello cold and cruel world

>>> print "hello","cold"+ " " + "and","cruel","world"

hello cold and cruel world

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Programming Workshop #1

Write a Python program to compute the hydrophobicity of an amino acid

Program will prompt the user for an amino acid and will display the hydrophobicity

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Solution to Programming Workshop 1 Write a Python program to compute the hydrophobicity of

an amino acid# Program to compute the hydrophobicity of an amino acid# (solution only includes first 3 amino acids)# Written by: Prof. Warter-Perez# Date created: April 15, 2004# Last modified:

hydro = {"A":1.8,"C":2.5,"D":-3.5}aa = raw_input ("Please enter amino acid: ")print "The hydrophobicity of %s is %f."% (aa, hydro[aa])

Introduction to Python – Part II 17

Make solution case insensitive

# Program to compute the hydrophobicity of an amino acid

# Written by: Prof. Warter-Perez

# Date created: April 15, 2004

# Last modified: April 20, 2004 - made script case insensitive for

# amino acids

hydro = {"A":1.8,"C":2.5,"D":-3.5}

aa = raw_input ("Please enter amino acid: ")

aa = aa.upper()

print "The hydrophobicity of %s is %f."% (aa, hydro[aa])

Introduction to Python – Part II 18

Python Basics – Relational and Logical Operators

Relational operators== equal!= not equal>greater than>= greater

than or equal

<less than<= less than or

equal

Logical operatorsand andor ornot not

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if Statement if expression:

actionExample:

a1 = 'A‘; a2 = 'C';match = 0;if (a1 == a2) :

match+=1;

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if-elif-else Statement if expression:

action 1elif expression:

action 2else :

action 3

Example:a1 = 'A‘; a2 = 'C';match = 0; gap = 0;if (a1 == a2) :

match+=1;elif (a1 > a2):

else:gap+=1;

Introduction to Python – Part II 21

for Statementfor var in list:

action Sets var to each item

in list and performs action

range() function generates lists of numbers: range (5) -> [0,1,2,3,4]

Examplemylist=[“hello”,”hi”,”hey”

,”!”];for i in mylist:

print i

Iteration 1 prints: hello

Iteration 2 prints: hi

Iteration 3 prints: hey

Iteration 4 prints: !

Introduction to Python – Part II 22

while Statement

while expression:action

Examplex = 0;while x != 3:

x = x + 1

Iteration 1: x=0+1=1Iteration 2: x=1+1=2Iteration 3: x=2+1=3Iteration 4: don’t exec

/ 2Infinite loop!

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Example: Amino Acid Search Write a program to count the number

of occurrences of an amino acid in a sequence. The program should prompt the user for

A sequence of amino acids (seq) The search amino acid (aa)

The program should display the number of times the search amino acid (aa) occurred in the sequence (seq)

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Example: Amino Acid Search (2)#this program will calculate the number of occurrences of an amino acid in a

#sequence

#by Bryce Ready

done=0

while (not done):

sequence=raw_input("Please enter a sequence:");

aa=raw_input("Please enter the amino acid to look for:");

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Example: Amino Acid Search (3) #compute the number of occurrences using for loop

cnt=0

for i in sequence:

if i == aa:

cnt+=1

if cnt == 1:

print "%s occurs in that sequence once" % aa

else:

print "%s occurs in that sequence %d times" % (aa, cnt)

answer=raw_input("try again? [yn]")

if answer == "n" or answer == "N":

done = 1

Introduction to Python – Part II 26

Programming Workshop #2

Write a sliding window program to compute the %GC in a sequence of nucleotides. The program should prompt the user for

The DNA sequence The window size (assume the window increment is 1)