1. An Introduction to Python – Part II Dr. Nancy Warter-Perez

2. Introduction to Python – Part II2 Overview References Python Programming for the Absolute Beginner (PP) Learning Python (LP) Solution to Programming Workshop #1 If tests (PP Ch1, LP Ch 9) Loops (PP Ch1, LP Ch 10) for while Example amino acid search program Programming Workshop #2

3. Introduction to Python – Part II3 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])

4. Introduction to Python – Part II4 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])

5. Introduction to Python – Part II5 Python Basics - Comments Python comments # line comment Header comments #Description of program #Written by: #Date created: #Last Modified:

6. Introduction to Python – Part II6 Python Basics - Variables Python variables are not “declared”. To assign a variable, just type: identifier=literal Identifiers Have the following restrictions: Must start with a letter or underscore (_) Case sensitive Must consist of only letters, numbers or underscore Must not be a reserved word (LP pg 137) Have the following conventions: All uppercase letters are used for constants Variable names are meaningful – thus, often multi-word Convention 1: alignment_sequence Convention 2: AlignmentSequence Python specific conventions: Avoid _X, __X__, __X, _, (LP pg 138)

7. Introduction to Python – Part II7 Numbers Normal Integers –represent whole numbers Ex: 3, -7, 123, 76 Long Integers – unlimited size Ex: 9999999999999999999999L Floating-point – represent numbers with decimal places Ex: 1.2, 3.14159,3.14e-10 Octal and hexadecimal numbers Ex: O177, 0x9ff, Oxff Complex numbers Ex: 3+4j, 3.0+4.0j, 3J

8. Introduction to Python – Part II8 Python Basics – arithmetic operations +add -subract *multiply /divide %modulus/remainder y=5; z=3 x = y + z x = y – z x = y * z x = y / z x = y % z x = 8 x = 2 x = 15 x = 1 x = 2 OperatorsExample

9. Introduction to Python – Part II9 Python Basics – arithmetic operations << shift left >> shift right **raise to power y=5; z=3 x = y << 1 x = y >> 2 x = y ** z x = 10 x = 1 x = 125 OperatorsExample

10. Introduction to Python – Part II10 Python Basics – Relational and Logical Operators Relational operators ==equal !=, <>not equal >greater than >=greater than or equal <less than <=less than or equal Logical operatorsandornot

11. Introduction to Python – Part II11 Python Basics – Relational Operators Assume x = 1, y = 4, z = 14 ExpressionValueInterpretation x < y + z1True y == 2 * x + 30False z <= x + y0False z > x1True x != y1True

12. Introduction to Python – Part II12 Python Basics – Logical Operators Assume x = 1, y = 4, z = 14 ExpressionValueInterpretation x<=1 and y==30False x<= 1 or y==31True not (x > 1)1True not x > 10False not (x<=1 or y==3)0False

13. Introduction to Python – Part II13 Enclosed in single or double quotes Ex: ‘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…

14. Introduction to Python – Part II14 String operations mystring = “Hello World!” ExpressionValuePurpose len(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

15. Introduction to Python – Part II15 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!”

16. Introduction to Python – Part II16 Strings (3) “%” operator: sort of “fill in the blanks” operation: mystring=“%s has %d marbles” % (“John”,35) mystring -> “John has 35 marbles” %sreplace with string %d,%ireplace with integer %freplace with float Values to put in blanks “blanks”

17. Introduction to Python – Part II17 Lists mylist=[“a”,”b”,3.58,”d”,4,0] mylist[0] mylist[2] a 3.58 Indexing mylist[-1] mylist[-2] 0404 Negative indexing (counts from end) mylist[1:4][“b”,3.58,”d”]Slicing (like strings) “b” in mylist “e” not in mylist 1 or True mylist.append(8)[“a”,”b”,3.58,”d”,4,0,8]Add to end of list

18. Introduction to Python – Part II18 Tuples Tuples – sequence of values like lists, but cannot be changed after it is created mytuple=(1,”a”,”bc”,3,87.2) mytuple[2] -> “bc” mytuple[1]=“3” Used when you want to pass several variables around at once Error!

19. Introduction to Python – Part II19 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’] -> 3 mydict[75] -> 2.85 mydict[‘a’] -> 4

20. Introduction to Python – Part II20 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”]3.5Value lookup mydict.has_key(“r”)True or 1Check for keys mydict.update({“a”:75}){8.5: 8, 'a': 75, 'r': 1, 'g': 2, 'y': 3.5, 9: 'nine'} Add pairs to dictionary

21. Introduction to Python – Part II21 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 " ", line 1, in ? KeyError: 'red‘ Use mydict.get(“red”) instead, it returns None if key is not found

22. Introduction to Python – Part II22 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!'

23. Introduction to Python – Part II23 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!

24. Introduction to Python – Part II24 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

25. Introduction to Python – Part II25 Python Basics – Relational and Logical Operators Relational operators ==equal !=not equal >greater than >=greater than or equal <less than <=less than or equal Logical operatorsandornot

26. Introduction to Python – Part II26 if Statement if expression: action Example: a1 = 'A‘; a2 = 'C'; match = 0; if (a1 == a2) : match+=1;

27. Introduction to Python – Part II27 if-elif-else Statement if expression: action 1 elif expression: action 2 else : action 3 Example: a1 = 'A‘; a2 = 'C'; match = 0; gap = 0; if (a1 == a2) : match+=1; elif (a1 > a2): else: gap+=1;

28. Introduction to Python – Part II28 for Statement for 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] Example mylist=[“hello”,”hi”,”hey”,”!”]; for i in mylist: print i Iteration 1 prints: hello Iteration 2 prints: hi Iteration 3 prints: hey Iteration 4 prints: !

29. Introduction to Python – Part II29 while Statement while expression: action Example x = 0; while x != 3: x = x + 1 Iteration 1: x=0+1=1 Iteration 2: x=1+1=2 Iteration 3: x=2+1=3 Iteration 4: don’t exec / 2 Infinite loop!

30. Introduction to Python – Part II30 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)

31. Introduction to Python – Part II31 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:");

32. Introduction to Python – Part II32 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

33. Introduction to Python – Part II33 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)