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MEIN 50010: Python – Introduction

Fabian Sievers

Higgins Lab, Conway Institute

University College Dublin

Wednesday, 2017-10-04

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Outline

Goals

Teach basic programming concepts

Apply these concepts using Python

Use Python Packages and libraries

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What is Computer Programming?

Writing software

Multistep process to solve a problem• Formulate the problem

• Generate set of steps to solve problem⇒ Algorithm

• Verify Algorithm⇒ Correctness, resource requirements

• Implementation⇒ Write code in programming language

• Testing/Debugging⇒ Coverage

• Distribution/Documentation/Maintenance

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Purpose of Programming

Generate sequence of instructions that solve a problemor automate a task• Excellent practice of critical/logical thinking• Modern biology is data intensive• Everyday life is IT intensive → good skill to have

Implement in a programming language• C/C++• Java• Perl• PHP• Python• and many, many more . . .

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Python

High level language, handles grunt work• Clean, concise, unambiguous syntax• Rapid application development

Interpreted language, Open source, Flexible, Scalable

Many resources (libraries, tutorials, forums)• https://docs.python.org• https://stackoverflow.com/questions/tagged/python• http://www.diveintopython3.net/ (book)

Large communityofficial Google languageincreasing bioinfo usage...

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Interpreted vs Compiled

Python (looks like English):print("Hello World!")

C (needs to be compiled):include <stdio.h>

int main(int argc, char *argv[]){

printf("Hello World!\n");

return 0;

}

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Low Level Language

Assembly (what the computer likes):.model tiny

.data

message db ’Hello, World!’

.code

org 100h

start:

mov ah,9

mov dx,offset message

int 21h

ret

end start

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A Bit about Bits

There are 10 kinds of peopleThose who understand binaryAnd those who don’t

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What is a Bit?

Computer microprocessor (CPU) composed of manyswitches called bits

Two configurations for a switch• ’on’ or ’off’• ’true’ or ’false’• ’0’ or ’1’

Combine/manipulate bits with Boolean algebra• and ∧, or ∨, not ¬• build up other operations with these

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What is a Byte?Usually, 1 Byte = 8 bits

Smallest addressable unit of memoryRepresent integers (base 10) by their powers of 2• 010 = 000000002 →

0×27+0×26+0×25+0×24+0×23+0×22+0×21+0×20

• 110 = 000000012 →0×128+0×64+0×32+0×16+0×8+0×4+0×2+1×1

• 210 = 000000102 →0×128+0×64+0×32+0×16+0×8+0×4+1×2+0×1

• 310 = 000000112 →0×128+0×64+0×32+0×16+0×8+0×4+1×2+1×1

•...

• 25510 = 111111112 →1×128+1×64+1×32+1×16+1×8+1×4+1×2+1×1

Floating Point Number• binary expansion of 0.1 doesn’t terminate, same as

decimal expansion of 1/3 (0.333 . . .)0.110 = 0/2 + 0/4 + 0/8 + 1/16 + 1/32 + 0/64 +0/128 + 1/256 + 1/512 . . .10 = 0.000110011 . . .2

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Variables

A Variable is an object that stores data which canchange

Program can’t do anything useful without variablescan only do one thing, no flexibility

Declare it (name it)• name refers to location in memory• name can be whatever you like (should be descriptive,

reflect scope, conform to local standards)• in Python name must begin with letter• in Python name cannot be reserved (key) word

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Data Types

integer: number of sheep = 39

maximum value (depending on platform)231 − 1 = 2, 147, 483, 647 (32-bit) or263 − 1 ≈ 9.2× 1018 (64-bit)

float: weight = 75.4

maximum value ≈ 1.8× 10308

Boolean: Answer = False

complex: phase = 3+2j

String: greeting = ’Hello World!’

a sequence of characters surrounded by (single, doubleor triple) quotes

Collection of variablesList: elements = [’H’, ’He’, ’Li’, ’Be’]

Dictionary: GerEng = {’Hund’:’dog’,

’Katze’:’cat’}

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Dynamic Typing

Python uses dynamic typing model for variables

• Variables don’t need to be declared in advance• Variables don’t have a type associated with them,

values do>>>x = 2 # x refers to an integer>>>x = ’Hello’ # now x refers to a string>>>x = True # and now to a Boolean

Python uses strong dynamic typing• Applying operations to incompatible types is not

permitted>>>1 + ’hello’

Traceback (most recent call last):

File ‘‘<stdin>’’, line 1, in <module>

TypeError: unsupported operand type(s) for

+: ’int’ and ’str’

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Basic Operators

Can’t do anything with varibles unless we haveoperators

Operators are tokens which carry out ’operations’ ondata/variables

Assign a value with the assignment operator ’=’a=5

Mathematical operators+ - * / ** % //

Comparison operators== != > < >= <=

String operatorsconcatenate +, repeat *, slice [:]

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Basic Operators

Addition: +

>>>2+3 ⇒ 5

Subtraction: -

>>>2-3 ⇒ -1

Multiplication: * (asterisk)>>>2*3 ⇒ 6

Division: /

>>>2/3 ⇒ 0.6666666666666666

Exponent: **

>>>2**3 ⇒ 8

>>>2**0.5 ⇒ 1.4142135623730951

Modulo: % (remainder)>>>14%4 ⇒ 2 (14 = 3 * 4 + 2)

Integer Division: //

>>>14//4 ⇒ 3 (14 = 3 * 4 + 2)

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Boolean Expressions

Equal to: == (note double-equal sign)>>>2 == 3 ⇒ False

>>>3 == 3 ⇒ True

Not equal to: !=

>>>2 != 3 ⇒ True

>>>3 != 3 ⇒ False

Less than: <

>>>2 < 3 ⇒ True

>>>3 < 3 ⇒ False

Less than or equal: <=

>>>2 <= 3 ⇒ True

>>>3 <= 3 ⇒ True

>>>4 <= 3 ⇒ False

Greater / Greater or equal: > / >=

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Boolean Expressions

Test multiple conditions with and

Only true if both conditions met>>>(1 < 2) and (3 < 4) ⇒ True

>>>(1 < 2) and (3 < 3) ⇒ False

Test multiple conditions with or

True if either condition met>>>(1 < 2) or (3 < 3) ⇒ True

>>>(1 > 2) or (3 > 4) ⇒ False

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Operator precedence

In mathematics multiplication before addition1 + 2× 3 = 1 + (2× 3) = 7 6= (1 + 2)× 3 = 9

Same precedence in Python (and other languages)

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Functions

A function performs specific task on data stored invariable

Main purpose of this course is to learn how to writeyour own functions

Python has ’built-in’ functions

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Functions

abs(x) – Return the absolute value of a number

bin(x) – Convert an integer number to a binary string

input([prompt]) – Write prompt to standard output,then read a line from input

len(s) – Return the length (the number of items) ofan object

open(file, mode) – Open file and return file object

print(objects, file) – Print objects to the textstream file...

Sometimes you will see object.method(arg), e.g.,’Hello World’.find(’W’) – essentially same asfunction

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Counting

Computer scientists use zero based counting>>>’Hello World’.find(’H’)

0

Slice index goes from start index up to but notincluding end index>>>’Hello World’[1:4]

’ell’

>>>’Hello World’[:4]

’Hell’

>>>’Hello World’[7:]

’orld’

Slice from end using negative index>>>’Hello World’[-1]

’d’

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Using Python

Python can be used in 2 ways:

Interactive Python Interpreter• Write-as-you-go mode, useful for learning and testing

small programs• Typed statements are evaluated immediately

Write and run script files• Create script file with list of Python commands• Use plain text editor to create/modify script• Contents of script are evaluated line by line as script is

run

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The Python InterpreterStarting the Python Interpreter

Linux/Unix• Open terminal window (gnome, konsole, xterm) and

type python3

Mac OSX• Open terminal and type python3

Windows• From Start Menu search for cmd• Type python

We are using Python 3 not 2.6/2.7

Line starting with >>> (or ...) are printed by interpreter

Line not starting with >>> is output

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Using Python interactively

Exit interpreter with quit()

alternatively• Mac/Linux: Control-D• Windows: Control-Z followed by return

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Using Python ScriptsSecond way to use PythonCreate script file with list of Python commandsUse plain text editor to create file• Linux: GEdit, Emacs, Vi, . . .• Mac OSX: TextEdit, TextWrangler, Vi, . . .• Windows: Notepad++• Python inbuilt: IDLE

• Windows: All Programs → Python3.X → IDLE• IDLE displays Python interpreter window• to begin script, choose menu File → New Window• start typing script, when done, menue File → Save• to execute, choose menu Run → Run Module• output written to interpreter window

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Python + Command Prompt

Python scripts can be run from Windows commandprompt

Select Programs → Accessories → Command Prompt(or search for cmd)

You may need to tell Wndows where to find PythonC:\> set path=%path%;C:\Python34

Change to directory containing your Python scriptC:\> cd mein50010

Run script by passing filename as argumentC:\mein50010\> python hello.py

Mac & Linux work similarly

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Credits

Interpreted vs Compiled figure – Peadar O’Gaora lectureGENE 30040

Assembly version ’Hello World’ –www.codecodex.com/wiki/Hello world

Python keywords –docs.python.org/3/reference/lexical analysis.html

Operator precedence –docs.python.org/3/reference/expressions.html

Built-in functions –docs.python.org/3/library/functions.html

Truth table – en.wikipedia.org/wiki/Boolean algebra

Colm Ryan – COMP50050