1. An Introduction to Python and Its Use in Bioinformatics Dr. Nancy Warter-Perez

2. Introduction to Python2 Overview What is Bioinformatics? Overview of program/script development Python Basics Python Types and Operators Numbers and Arithmetic operators Strings, Lists, and Dictionaries Input & Output Programming Workshop #1

3. Introduction to Python3 What is Bioinformatics? Fredj Tekaia at the Institut Pasteur offers this definition of bioinformatics:Institut Pasteur "The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information."

4. Introduction to Python4 Bioinformatics http://www.stat.purdue.edu/images/bioinformatics/ Bioinformatics_doerge_080304%20(1)-sm.jpg

5. Introduction to Python5 Program Development Problem specification Algorithm design Test by hand Code in target language Test code / debug Program/Script Problem solving Implementation

6. Introduction to Python6 What is Python? A portable, interpretive, object-oriented programming language Elegant syntax Powerful high-level built-in data types Numbers, strings, lists, dictionaries Full set of string operations

7. Introduction to Python7 Why Python? Previously used C++ Scripting languages useful for bioinformatics Perl often thought of as “bioinformatics standard” Python is more “robust” for larger software projects

8. Introduction to Python8 Useful Tutorials DNA from the Beginning http://www.dnaftb.org/dnaftb/ Python Tutorial http://www.python.org/doc/current/tut/tut.html

9. Introduction to Python9 Python Development Open- Source Software Python interpreter - will run on windows, you need to download it in two parts: 1. the actual interpreter and core of python http://www.python.org/download/releases/2.5.2/ http://www.python.org/download/releases/2.5.2/ 2. an integrated development environment for python called pythonwin, by Mark Hammond http://sourceforge.net/projects/pywin32/ http://sourceforge.net/projects/pywin32/

10. Introduction to Python10 Python Basics - Comments Python comments # line comment Header comments #Description of program #Written by: #Date created: #Last Modified:

11. Introduction to Python11 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)

12. Introduction to Python12 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

13. Introduction to Python13 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

14. Introduction to Python14 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

15. Introduction to Python15 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

16. Introduction to Python16 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

17. Introduction to Python17 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

18. Introduction to Python18 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…

19. Introduction to Python19 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

20. Introduction to Python20 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!”

21. Introduction to Python21 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”

22. Introduction to Python22 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

23. Introduction to Python23 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!

24. Introduction to Python24 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

25. Introduction to Python25 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

26. Introduction to Python26 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

27. Introduction to Python27 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!'

28. Introduction to Python28 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!

29. Introduction to Python29 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

30. Introduction to Python30 Creating a Python Program Enter your program in the editor Notice that the editor has a color coding Comments Key words Etc… Also notice that it automatically indents Don’t override!! – this is how python tells when block statements end! If doesn’t indent to proper location – indicates bug

31. Introduction to Python31 Running your Program To build your program Under File->Run… Select No Debugging in the drop-down window Fix any errors, then run again

32. Introduction to Python32 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