PythonLecture1_08

8/12/2019 PythonLecture1_08

1/30

An Introduction to Python and ItsUse in Bioinformatics

Dr. Nancy Warter-Perez


2/30

Introduction to Python 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


3/30


Program DevelopmentProblem specification

Algorithm design

Testby hand

Code in target language

Testcode / debug

Program/Script

Problemsolving

Implementation


4/30


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


5/30


Why Python? Previously used C++

Scripting languages useful for

bioinformatics

Perl was bioinformatics standard

Python is more robust for largersoftware projects


6/30


Useful Tutorials DNA from the Beginning

http://www.dnaftb.org/dnaftb/

Python Tutorial

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


7/30Introduction to Python 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 pythonhttp://www.python.org/download/releases/2.5/(were using python-2.3.3 in class).

2. An integrated development environment for

python called pythonwin, by Mark Hammondhttp://sourceforge.net/project/showfiles.php?group_id=78018
http://www.python.org/download/releases/2.5/http://www.python.org/download/releases/2.5/http://sourceforge.net/project/showfiles.php?group_id=78018http://sourceforge.net/project/showfiles.php?group_id=78018http://sourceforge.net/project/showfiles.php?group_id=78018http://sourceforge.net/project/showfiles.php?group_id=78018http://www.python.org/download/releases/2.5/http://www.python.org/download/releases/2.5/



Python Basics - Comments Python comments

# line comment

Header comments

#Description of program

#Written by:

#Date created:

#Last Modified:



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 meaningfulthus, often multi-word (but nottoo long)

Convention 1: alignment_sequence (align_seq)

Convention 2: AlignmentSequence (AlignSeq)

Python specific conventions (Avoid _X, __X__, __X, _)



Numbers Numbers

Normal Integersrepresent whole numbersEx: 3, -7, 123, 76

Long Integersunlimited sizeEx: 9999999999999999999999L

Floating-pointrepresent numbers with decimalplaces

Ex: 1.2, 3.14159,3.14e-10 Octal and hexadecimal numbers

Ex: O177, 0x9ff, Oxff

Complex numbersEx: 3+4j, 3.0+4.0j, 3J



Python Basicsarithmetic operations

+ add

- subract

* multiply/ divide

% modulus/remainder

y=5; z=3

x = y + z

x = yz

x = y * zx = y / z

x = y % z

x = 8

x = 2

x = 15x = 1

x = 2

Operators Example



Python Basicsarithmetic operations

> shift right

** raise to power

y=5; z=3

x = y > 2

x = y ** z

x = 10

x = 1

x = 125

Operators Example



Python BasicsRelational and

Logical Operators

Relational operators

== equal

!=, not equal

> greater than

>= greater than or

equal< less than


14/30


Python BasicsRelational

OperatorsAssume x = 1, y = 4, z = 14

Expression Value Interpretation

x < y + z 1 True

y == 2 * x + 3 0 False

z x 1 True

x != y 1 True


15/30


Python BasicsLogical

OperatorsAssume x = 1, y = 4, z = 14

Expression Value Interpretation

x 1 0 False

not (x


16/30


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


17/30


String operationsmystring = Hello World!

Expression Value Purpose

len(mystring) 12 number of characters inmystring

hello+world helloworld Concatenate strings

%s world%hello hello world Format strings (like sprintf)

world == hello

world == world0 or False1 or True

Test for equality

a < b

b < a

1 or True

0 or False

Alphabetical ordering


18/30


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!


19/30


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 putin blanks

blanks


20/30


Listsmylist=[a,b,3.58,d,4,0]

mylist[0]

mylist[2]

a

3.58

Indexing

mylist[-1]

mylist[-2]

0

4

Negative indexing(counts from end)

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

b in myliste notinmylist

1 or True1 or True

mylist.append(8) [a,b,3.58,d,4,0,8] Add to end of list


21/30


Tuples Tuplessequence 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 severalvariables around at once

Error!


22/30


Dictionaries Dictionariesmap 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] -> 2.85

mydict[a] -> 4


23/30


Dictionariesmydict={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 valuesmydict[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 todictionary


24/30


Dictionariesother

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 "", line 1, in ?

KeyError: 'redUse mydict.get(red) instead, it returns None if

key is not found


25/30


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!'


26/30


Output Function print

Prints eachargument, followedby space

After all arguments,prints newline

Put comma after last

arg to preventnewline

add strings to avoidspaces

printa,b,c

a b c

print a,b,c,

a b c

print a+b+c

abc

Newline!

NoNewline!

Nospaces!


27/30


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


28/30


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

Dont override!! this is how python tells when block

statements end!

If doesnt indent to proper location indicates bug


29/30


Running your Program To build your program

Under File->Run

Select No Debugging in the drop-down window

Fix any errors, then run again


30/30

Int od ction to P thon 30

Workshop #6 Write a Python program to compute the

hydrophobicity of an amino acidA m ino A c id H y dr op . V A LU E

A 1.8

C 2.5D -3 .5

E -3 .5

F 2 .8

G -0 .4

H -3 .2

I 4 .5

K -3 .9

L 3 .8

M 1.9

N -3 .5

P -1 .6

Q -3 .5

R -4 .5

S -0 .8

T -0 .7

V 4.2

W -0 .9

Y -1 .3

Program will promptthe user for anamino acid and willdisplay thehydrophobicity

PythonLecture1_08

Documents

Transcript of PythonLecture1_08