An Introduction to Python and Its Use in Bioinformatics

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

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 Introduction to Python

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

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

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 Introduction to Python

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 Introduction to Python

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

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 (recommend Python 2.6.2) http://www.python.org/download/ 2. an integrated development environment for python called pythonwin, by Mark Hammond http://sourceforge.net/projects/pywin32/ Introduction to Python

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

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) Introduction to Python

Numbers • 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 Introduction to Python

Python Basics – arithmetic operations OperatorsExample + add - subract * multiply / divide % modulus/remainder ** raise to power y=5; z=3 x = y + z 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 x = 125 Introduction to Python

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

Python Basics – Relational Operators • Assume x = 1, y = 4, z = 14 Introduction to Python

Python Basics – Logical Operators • Assume x = 1, y = 4, z = 14 Introduction to Python

Strings • 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] -> “!” -1 is last, -2 next to last, etc… Introduction to Python

String operations Introduction to Python

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!” Introduction to Python

“blanks” Values to put in blanks 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 Introduction to Python

Lists Introduction to Python

Error! Tuples • Tuples – sequence of valueslike 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 Introduction to Python

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 Introduction to Python

Dictionaries Introduction to Python

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 Introduction to Python

Function raw_input() designed to input a line of input as a string 1 optional argument: string to prompt user If int or float desired, use function input() instead Can also easily convert strings to int and float using: int(mystring)->convert to int (if possible) float(mystring)->convert to float (if possible) Input/Output >>> mystr=raw_input("Enter a string:") Enter a string:Hello World! >>> mystr 'Hello World!' Introduction to Python – Part II

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! Output Introduction to Python

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 Introduction to Python

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 Introduction to Python

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

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 Introduction to Python

An Introduction to Python and Its Use in Bioinformatics