An Introduction to Python and Its

Use in Bioinformatics
Dr. Nancy Warter-Perez


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

Introduction to Python 3
Program Development
Problem specification
Algorithm design
Test by hand
Code in target language
Test code / debug
Program/Script
Problem
solving
Implementation
Introduction to Python 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
Introduction to Python 5
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 6
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 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/2.5/
(were 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?grou
p_id=78018
Introduction to Python 8
Python Basics - Comments
Python comments
# line comment
Header comments
#Description of program
#Written by:
#Date created:
#Last Modified:
Introduction to Python 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, _)
Introduction to Python 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
Introduction to Python 11
Python Basics arithmetic operations

+ 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
x = 2
Operators Example
Introduction to Python 12
Python Basics arithmetic operations

<< 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
Operators Example
Introduction to Python 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
Introduction to Python 14
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
Introduction to Python 15
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
Introduction to Python 16
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] -> !
Strings
-1 is last,
-2 next to last, etc
Introduction to Python 17
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
1 or True
0 or False
Alphabetical ordering
Introduction to Python 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!


Introduction to Python 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
Values to put
in blanks
blanks
Introduction to Python 20
Lists
mylist=[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 mylist
e not in mylist
1 or True
1 or True
mylist.append(8) [a,b,3.58,d,4,0,8] Add to end of list
Introduction to Python 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
Error!
Introduction to Python 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
Introduction to Python 23
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 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
Introduction to Python 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)
>>> mystr=raw_input("Enter a string:")
Enter a string:Hello World!
>>> mystr
'Hello World!'
Introduction to Python 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
Newline!
No
Newline!
No
spaces!
Introduction to Python 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

Introduction to Python 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
Dont override!! this is how python tells when block
statements end!
If doesnt indent to proper location indicates bug
Introduction to Python 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
Introduction to Python 30
Workshop #6
Write a Python program to compute the
hydrophobicity of an amino acid


A m i no A c i d Hy drop . V A LUE
A 1. 8
C 2. 5
D - 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 prompt
the user for an
amino acid and will
display the
hydrophobicity