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

Introduction to Python Overview Overview of program/script development (BP Ch 1) Python Basics (BP Ch1) Python Types and Operators Numbers and Arithmetic operators (BP Ch1, App B) Strings (BP Ch3) Lists and Dictionaries (BP Ch2 and Ch4) Input & Output (BP Ch1) Programming Workshop #1 Introduction to Python

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

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

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

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 http://www.python.org/download/releases/ (we’re using python-2.3.3 in class). 2. An integrated development environment for python called pythonwin, by Mark Hammond http://sourceforge.net/project/showfiles.php?group_id=78018 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 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, _) Introduction to Python

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 Operators Example + 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 Introduction to Python

Python Basics – arithmetic operations Operators Example << 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 Introduction to Python

Python Basics – Relational and Logical Operators 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 Introduction to Python

Python Basics – Relational Operators Assume x = 1, y = 4, z = 14 Expression Value Interpretation x < y + z 1 True y == 2 * x + 3 False z <= x + y z > x x != y Introduction to Python

Python Basics – Logical Operators Assume x = 1, y = 4, z = 14 Expression Value Interpretation x<=1 and y==3 False x<= 1 or y==3 1 True not (x > 1) not x > 1 not (x<=1 or y==3) Introduction to Python

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 mystring = “Hello World!” Expression Value Purpose 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” Alphabetical ordering Introduction to Python

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

Introduction to Python 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 “blanks” Values to put in blanks Introduction to Python

Introduction to Python Lists mylist=[“a”,”b”,3.58,”d”,4,0] mylist[0] mylist[2] a 3.58 Indexing mylist[-1] mylist[-2] 4 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 Introduction to Python

Introduction to Python 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! Introduction to Python

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’] -> 3 mydict[75] -> 2.85 mydict[‘a’] -> 4 Introduction to Python

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 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

Introduction to Python 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!' Introduction to Python

Introduction to Python 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”, print “a”+”b”+”c” abc Newline! No Newline! No spaces! Introduction to Python

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" 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

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

Introduction to Python Workshop #1P 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