1	An Introduction to Python and Its Use in Bioinformatics Dr. Nancy Warter-Perez
2	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
3	Program Development
4	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
5	Why Python? Previously used C++ Scripting languages useful for bioinformatics Perl was “bioinformatics standard” Python is more “robust” for larger software projects
6	Useful Tutorials DNA from the Beginning http://www.dnaftb.org/dnaftb/ Python Tutorial http://www.python.org/doc/current/tut/tut.html
7	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
8	Python Basics - Comments Python comments # line comment Header comments #Description of program #Written by: #Date created: #Last Modified:
9	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, _)
10	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
11	Python Basics – arithmetic operations + add - subract * multiply / divide % modulus/remainder
12	Python Basics – arithmetic operations << shift left >> shift right ** raise to power
13	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
14	Python Basics – Relational Operators Assume x = 1, y = 4, z = 14
15	Python Basics – Logical Operators Assume x = 1, y = 4, z = 14
16	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] -> “!”
17	String operations
18	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!”
19	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
20	Lists
21	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
22	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
23	Dictionaries
24	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
25	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)
26	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
27	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
28	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
29	Running your Program To build your program Under File->Run… Select No Debugging in the drop-down window Fix any errors, then run again
30	Workshop #2 Write a Python program to compute the hydrophobicity of an amino acid