An Introduction to Python and Its Use in Bioinformatics Dr. Nancy Warter-Perez April 19, 2005

4/19/05Introduction to Python2 Overview What is Bioinformatics? Overview of program/script development (PP Ch3) Python Basics (PP Ch1) Python Types and Operators Numbers and Arithmetic operators (PP Ch2) Strings (PP Ch4) Lists and Dictionaries (PP Ch5) Input & Output (PP Ch2) Programming Workshop #1

4/19/05Introduction 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."

4/19/05Introduction to Python4 Classical Bioinformatics According to Damian Counsell from bioinformatics.orgDamian Counsell “use computers to store, retrieve, analyze or predict the composition or the structure of biomolecules. As computers become more powerful you could probably add simulate to this list of bioinformatics verbs. "Biomolecules" include your genetic material---nucleic acids---and the products of your genes: proteins. These are the concerns of "classical" bioinformatics, dealing primarily with sequence analysis.”

4/19/05Introduction to Python5 “New” Bioinformatics comparative genomics - look for differences and similarities between all the genes of multiple species functional genomics - identifying gene functions and associations proteomics - catalogue the activities and characterize interactions between all gene products (in humans) structural genomics - crystallize and or predict the structures of all proteins (in humans)

4/19/05Introduction to Python6 Program Development Problem specification Algorithm design Test by hand Code in target language Test code / debug Program/Script Problem solving Implementation

4/19/05Introduction to Python7 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

4/19/05Introduction to Python8 Why Python? Previously used C++ Scripting languages useful for bioinformatics Perl is “bioinformatics standard” Python is more “robust” for larger software projects

4/19/05Introduction to Python9 Useful Tutorials DNA from the Beginning Python Tutorial

4/19/05Introduction to Python10 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 (get the Python exe file. There is a newer release (2.4.1) that you can download if you’d prefer.) 2. An integrated development environment for python called pythonwin, by Mark Hammond 2/Downloads.html 2/Downloads.html

4/19/05Introduction to Python11 Python Basics - Comments Python comments # line comment Header comments #Description of program #Written by: #Date created: #Last Modified:

4/19/05Introduction to Python12 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 Have the following conventions: All uppercase letters are used for constants Variable names are meaningful – thus, often multi-word (but not too long) Convention 1: alignment_sequence (align_seq) Convention 2: AlignmentSequence (AlignSeq) Python specific conventions (Avoid _X, __X__, __X, _)

4/19/05Introduction to Python13 Numbers Normal Integers –represent whole numbers Ex: 3, -7, 123, 76 Long Integers – unlimited size Ex: L Floating-point – represent numbers with decimal places Ex: 1.2, ,3.14e-10 Octal and hexadecimal numbers Ex: O177, 0x9ff, Oxff Complex numbers Ex: 3+4j, j, 3J

4/19/05Introduction to Python14 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

4/19/05Introduction to Python15 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

4/19/05Introduction to Python16 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

4/19/05Introduction to Python17 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

4/19/05Introduction to Python18 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

4/19/05Introduction to Python19 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…

4/19/05Introduction to Python20 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

4/19/05Introduction to Python21 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!”

4/19/05Introduction to Python22 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”

4/19/05Introduction to Python23 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

4/19/05Introduction to Python24 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!

4/19/05Introduction to Python25 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

4/19/05Introduction to Python26 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

4/19/05Introduction to Python27 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

4/19/05Introduction to Python28 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!'

4/19/05Introduction to Python29 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!

4/19/05Introduction to Python30 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

4/19/05Introduction to Python31 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

4/19/05Introduction to Python32 Running your Program To build your program Under File->Run… Select No Debugging in the drop-down window Fix any errors, then run again

4/19/05Introduction to Python33 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