An Introduction to Python and Its Use in Bioinformatics

Dr. Nancy Warter-PerezApril 19, 2005

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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

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What is Bioinformatics? Fredj Tekaia at the Institut Pasteur

offers this definition of bioinformatics:"The mathematical, statistical and computing methods that aim to solve biological problems using DNA and amino acid sequences and related information."

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Classical Bioinformatics According to Damian Counsell from

bioinformatics.org“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.”

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“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)

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Program DevelopmentProblem specification

Algorithm design

Test by hand

Code in target language

Test code / debug

Program/Script

Problem solving

Implementation

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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

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Why Python? Previously used C++ Scripting languages useful for

bioinformatics Perl is “bioinformatics standard” Python is more “robust” for larger

software projects

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Useful Tutorials DNA from the Beginning

http://www.dnaftb.org/dnaftb/ Python Tutorial

http://www.python.org/doc/current/tut/tut.html

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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/2.3.3/ (get the Python-2.3.3.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 http://starship.python.net/crew/mhammond/win32/Downloads.html

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Python Basics - Comments Python comments

# line comment Header comments

#Description of program#Written by:#Date created:#Last Modified:

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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, _)

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Numbers Numbers

Normal Integers –represent whole numbers Ex: 3, -7, 123, 76

Long Integers – unlimited sizeEx: 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

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Python Basics – arithmetic operations

+ add- subract* multiply/ divide% modulus/remainder

y=5; z=3x = y + z x = y – z x = y * z x = y / z x = y % z

x = 8x = 2x = 15x = 1x = 2

OperatorsExample

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Python Basics – arithmetic operations

<< shift left

>> shift right** raise to power

y=5; z=3x = y << 1 x = y >> 2 x = y ** z

x = 10x = 1x = 125

OperatorsExample

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Python Basics – Relational and Logical Operators

Relational operators== equal!=, <> not equal>greater than>= greater

than or equal

<less than<= less than or

equal

Logical operatorsand andor ornot not

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

Expression Value Interpretation

x < y + z 1 True

y == 2 * x + 3

0 False

z <= x + y 0 False

z > x 1 True

x != y 1 True

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

Expression Value Interpretation

x<=1 and y==3 0 False

x<= 1 or y==3 1 True

not (x > 1) 1 True

not x > 1 0 False

not (x<=1 or y==3)

0 False

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Enclosed in single or double quotesEx: ‘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…

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String operations

mystring = “Hello World!”

Expression Value Purposelen(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

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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!”

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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

Values to put in blanks

“blanks”

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Lists

mylist=[“a”,”b”,3.58,”d”,4,0]mylist[0]mylist[2]

a3.58

Indexing

mylist[-1]mylist[-2]

04

Negative indexing (counts from end)

mylist[1:4] [“b”,3.58,”d”] Slicing (like strings)

“b” in mylist“e” not in mylist

1 or True1 or True

mylist.append(8) [“a”,”b”,3.58,”d”,4,0,8]

Add to end of list

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Tuples Tuples – sequence of values

like 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

Error!

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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

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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

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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

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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!'

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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!

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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

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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

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Running your Program To build your program

Under File->Run… Select No Debugging in the drop-down

window Fix any errors, then run again

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Programming Workshop #1

Write a Python program to compute the hydrophobicity of an amino acid

Amino Acid Hydrop. VALUEA 1.8C 2.5D -3.5E -3.5F 2.8G -0.4H -3.2I 4.5K -3.9L 3.8M 1.9N -3.5P -1.6Q -3.5R -4.5S -0.8T -0.7V 4.2W -0.9Y -1.3

Program will prompt the user for an amino acid and will display the hydrophobicity