1. An Introduction to Python and Its Use in Bioinformatics
Dr. Nancy Warter-Perez

2. Introduction to Python
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. Introduction to Python
Program Development
Problem solving
Problem specification
Algorithm design
Test by hand
Implementation
Code in target language
Test code / debug
Program/Script
Introduction to Python

4. Introduction to Python
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. Introduction to Python
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. Introduction to Python
Useful Tutorials
DNA from the Beginning
Python Tutorial
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 (we’re using python in class).
2. An integrated development environment for python called pythonwin, by Mark Hammond
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. Introduction to Python
Numbers
Numbers
Normal Integers –represent whole numbers
Ex: 3, -7, 123, 76
Long Integers – unlimited size
Ex: L
Floating-point – represent numbers with decimal places
Ex: 1.2, ,3.14e-10
Octal and hexadecimal numbers
Ex: O177, 0x9ff, Oxff
Complex numbers
Ex: 3+4j, j, 3J
Introduction to Python

11. Python Basics – arithmetic operations
Operators Example
+ 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
Introduction to Python

12. Python Basics – arithmetic operations
Operators Example
<< 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
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
False
z <= x + y
z > x
x != y
Introduction to Python

15. Python Basics – Logical Operators
Assume x = 1, y = 4, z = 14
Expression
Value
Interpretation
x<=1 and y==3
False
x<= 1 or y==3 1
True
not (x > 1)
not x > 1
not (x<=1 or y==3)
Introduction to Python

16. Introduction to Python
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] -> “!”
-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”
Alphabetical ordering
Introduction to Python

18. Introduction to Python
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. Introduction to Python
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
“blanks”
Values to put in blanks
Introduction to Python

20. Introduction to Python
Lists
mylist=[“a”,”b”,3.58,”d”,4,0]
mylist[0]
mylist[2] a
3.58
Indexing
mylist[-1]
mylist[-2] 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
mylist.append(8)
[“a”,”b”,3.58,”d”,4,0,8]
Add to end of list
Introduction to Python

21. Introduction to Python
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. Introduction to Python
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. Introduction to Python
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. Introduction to Python
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”,
print “a”+”b”+”c”
abc
Newline!
No Newline!
No spaces!
Introduction to Python

27. Introduction to Python
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"
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
Don’t override!! – this is how python tells when block statements end!
If doesn’t indent to proper location – indicates bug
Introduction to Python

29. Introduction to Python
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. Introduction to Python
Workshop #1P
Write a Python program to compute the hydrophobicity of an amino acid
Program will prompt the user for an amino acid and will display the hydrophobicity
Introduction to Python