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An Introduction to Python – Part II
Dr. Nancy Warter-Perez
Overview
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References
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Solution to Programming Workshop #1
If tests (PP Ch1, LP Ch 9)
Loops (PP Ch1, LP Ch 10)
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Python Programming for the Absolute Beginner (PP)
Learning Python (LP)
for
while
Example amino acid search program
Programming Workshop #2
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Solution to Programming Workshop 1
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#
#
#
#
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Write a Python program to compute the hydrophobicity of an
amino acid
Program to compute the hydrophobicity of an amino acid
(solution only includes first 3 amino acids)
Written by: Prof. Warter-Perez
Date created: April 15, 2004
Last modified:
hydro = {"A":1.8,"C":2.5,"D":-3.5}
aa = raw_input ("Please enter amino acid: ")
print "The hydrophobicity of %s is %f."% (aa, hydro[aa])
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Make solution case insensitive
# Program to compute the hydrophobicity of an amino acid
# Written by: Prof. Warter-Perez
# Date created: April 15, 2004
# Last modified: April 20, 2004 - made script case insensitive for
# amino acids
hydro = {"A":1.8,"C":2.5,"D":-3.5}
aa = raw_input ("Please enter amino acid: ")
aa = aa.upper()
print "The hydrophobicity of %s is %f."% (aa, hydro[aa])
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Python Basics - Comments
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Python comments
# line comment
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Header comments
#Description of program
#Written by:
#Date created:
#Last Modified:
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Python Basics - Variables
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Python variables are not “declared”.
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To assign a variable, just type: identifier=literal
Identifiers
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Have the following restrictions:
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Must start with a letter or underscore (_)
Case sensitive
Must consist of only letters, numbers or underscore
Must not be a reserved word (LP pg 137)
Have the following conventions:
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All uppercase letters are used for constants
Variable names are meaningful – thus, often multi-word
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Convention 1: alignment_sequence
Convention 2: AlignmentSequence
Python specific conventions:
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Avoid _X, __X__, __X, _, (LP pg 138)
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Numbers
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Numbers
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Normal Integers –represent whole numbers
Ex: 3, -7, 123, 76
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Long Integers – unlimited size
Ex: 9999999999999999999999L
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Floating-point – represent numbers with decimal
places
Ex: 1.2, 3.14159,3.14e-10
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Octal and hexadecimal numbers
Ex: O177, 0x9ff, Oxff
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Complex numbers
Ex: 3+4j, 3.0+4.0j, 3J
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Python Basics – arithmetic operations
Operators
Example
y=5; z=3
+ add
x=y+z x
- subract
x=y–z x
* multiply
x=y*z x
/ divide
x=y/z x
% modulus/remainder x = y % z x
Introduction to Python – Part II
=
=
=
=
=
8
2
15
1
2
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Python Basics – arithmetic operations
Operators
<< shift left
>> shift right
** raise to power
Example
y=5; z=3
x = y << 1 x = 10
x = y >> 2 x = 1
x = y ** z x = 125
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Python Basics – Relational and
Logical Operators
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Relational operators
==
!=, <>
>
>=
<
<=
equal
not equal
greater than
greater than or
equal
less than
less than or equal
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Logical operators
and
or
not
Introduction to Python – Part II
and
or
not
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Python Basics – Relational
Operators
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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
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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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Strings
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Enclosed in single or double quotes
Ex: ‘Hello!’ , “Hello!”, “3.5”, “a”, ‘a’
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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…
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String operations
mystring = “Hello World!”
Expression
Value
Purpose
len(mystring)
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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)
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slicing:
mystring = “spoon!”
mystring[2:] -> “oon!”
mystring[:3] -> “spo” #note last element is never included!
mystring[1:3]-> “po”
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Many useful built-in functions
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mystring.upper() -> “SPOON!”
mystring.replace(‘o’, ‘O’) -> “spOOn!”
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Strings (3)
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“%” operator:
sort of “fill in the blanks” operation:
mystring=“%s has %d marbles” % (“John”,35)
“blanks”
mystring -> “John has 35 marbles”
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%s
%d,%i
%f
Values to put
in blanks
replace with string
replace with integer
replace with float
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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]
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Add to end of list
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Tuples
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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” Error!
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Used when you want to pass several variables
around at once
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Dictionaries
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Dictionaries – map ‘keys’ to ‘values’
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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
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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'}
Introduction to Python – Part II
Add pairs to
dictionary
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Dictionaries – other
considerations
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Slicing not allowed
Referencing invalid key is an error:
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>>> 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
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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
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Function print
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Prints each
argument, followed
by space
After all arguments,
prints newline
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Put comma after last
arg to prevent
newline
“add” strings to avoid
spaces
print “a”,”b”,”c”
abc
Newline!
print “a”,”b”,”c”,
No
abc
Newline!
print “a”+”b”+”c”
No
abc
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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Python Basics – Relational and
Logical Operators
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Relational operators
==
!=
>
>=
<
<=
equal
not equal
greater than
greater than or
equal
less than
less than or equal

Logical operators
and
or
not
Introduction to Python – Part II
and
or
not
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if Statement
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if expression:
action
Example:
a1 = 'A‘; a2 = 'C';
match = 0;
if (a1 == a2) :
match+=1;
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if-elif-else Statement
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if expression:
action 1
elif expression:
action 2
else :
action 3
Example:
a1 = 'A‘; a2 = 'C';
match = 0; gap = 0;
if (a1 == a2) :
match+=1;
elif (a1 > a2):
else:
gap+=1;
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for Statement
for var in list:
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action
Sets var to each item in
list and performs action
range() function
generates lists of
numbers:
range (5) -> [0,1,2,3,4]
Example
mylist=[“hello”,”hi”,”hey”,”!”];
for i in mylist:
print i
Iteration 1 prints: hello
Iteration 2 prints: hi
Iteration 3 prints: hey
Iteration 4 prints: !
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while Statement
while expression:
action
Example
x = 0;
while x != 3:
x = x + 1/ 2
Infinite loop!
Iteration
Iteration
Iteration
Iteration
Introduction to Python – Part II
1:
2:
3:
4:
x=0+1=1
x=1+1=2
x=2+1=3
don’t exec
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Example: Amino Acid Search
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Write a program to count the number of
occurrences of an amino acid in a
sequence.
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The program should prompt the user for
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A sequence of amino acids (seq)
The search amino acid (aa)
The program should display the number of
times the search amino acid (aa) occurred
in the sequence (seq)
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Example: Amino Acid Search (2)
#this program will calculate the number of occurrences of an amino
acid in a
#sequence
#by Bryce Ready
done=0
while (not done):
sequence=raw_input("Please enter a sequence:");
aa=raw_input("Please enter the amino acid to look for:");
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Example: Amino Acid Search (3)
#compute the number of occurrences using for loop
cnt=0
for i in sequence:
if i == aa:
cnt+=1
if cnt == 1:
print "%s occurs in that sequence once" % aa
else:
print "%s occurs in that sequence %d times" % (aa, cnt)
answer=raw_input("try again? [yn]")
if answer == "n" or answer == "N":
done = 1
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Programming Workshop #2
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Write a sliding window program to compute
the %GC in a sequence of nucleotides.
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The program should prompt the user for
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The DNA sequence
The window size (assume the window increment is 1)
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