Introduction to Python

Prof. James H. Thomas

Use python interpreter for quick syntax tests.

Write your program with a syntax-highlighting text
editor.
Save your program in a known location and using .py
extension.
Use the command window (or terminal session) to run
your program (make sure you are in the same
directory as your program).

Getting started on the Mac

Start a terminal session
Type python
This should start the Python interpreter (often called
IDLE)
Use the Python interpreter to test simple things.
> python
Python 2.6.4 (something something)
details something something
Type "help", "copyright", "credits" or "license"
for more information.
>>> print Hello, world!
Hello, world!

Run your program

In your terminal, Ctrl-D out of the python interpreter
(or start a new terminal).
Type pwd to find your present working directory.
Open TextWrangler.
Create a file with your program text.
Be sure that you end the line with a carriage return.
Save the file as prog.py in your present working
directory.
In your terminal, type python prog.py
> python hello.py
hello, world!

Common beginner's mistakes

If your terminal prompt has three '>' characters you are in the Python
interpreter:

>>> print 7
7
>>>
To run a program, be sure you have a normal terminal prompt (will
vary by system), will usually end with a '$' or a single '>' character:
>>> python myprog.py arg1 arg2
(program output)

When you write your program (in a text editor), be sure to save it
before trying out the new version! Python reads the saved file to
run your program.

Summary of Command Line Basics

Run a program by typing at a terminal session command line prompt (which
may be > or $ or something else depending on your computer; it also may or
may not have some text before the prompt).
If you type 'python' at the prompt you will enter the Python IDLE
interpreter where you can try things out (ctrl-D to exit).
If you type 'python myprog.py' at the prompt, it will run the program
'myprog.py' if it is present in the present working directory.
'python myprog.py arg1 arg2' (etc) will provide command line
arguments to the program.

Each argument is a string object and they are accessed using sys.argv[0],
sys.argv[1], etc., where the program file name is the zeroth argument.
Write your program with a text editor and be sure to save it in the present
working directory before running it.

Objects and types

An object refers to any entity in a python program.

Every object has an associated type, which determines the properties
of the object.
Python defines six types of built-in objects:
Number
String
List
Tuple
Dictionary
File

10 or 2.71828
hello
[1, 17, 44] or [pickle, apple, scallop]
(4, 5) or (homework, exam)
{food : something you eat, lobster : an edible arthropod}
more later

It is also possible to define your own types, comprised of combinations

of the six base types.

Literals and variables

A variable is simply a name for an object.
For example, we can assign the name pi to the
Number object 3.14159, as follows:

>>> pi = 3.14159
>>> print pi
3.14159
When we write out the object directly, it is a literal,
as opposed to when we refer to it by its variable
name.

The command line

The command line is the text you enter after the
word python when you run a program.
python my-program.py GATTCTAC 5
The zeroth argument is the name of the program file.
Arguments larger than zero are subsequent elements
of the command line.
zeroth
argument

first
argument

second
argument

Reading command line arguments

Access in your program like this:
import sys
print sys.argv[0]
print sys.argv[1]

zeroth
argument
first
argument

> python my-program.py 17

my-program.py
17
There can be any number of arguments, accessed
by sequential numbers (sys.argv[2] etc).

Assigning variables
In order to retain program access to a value,
you have to assign it to a variable name.
this says give me access to all
the stuff in the sys module
import sys
sys.argv[0]

this doesnt do anything it says get the

string that is stored at index 0 in the list
sys.argv and do nothing with it

import sys
print sys.argv[0]

this says get the string that is stored at

index 0 in the list sys.argv and print it
(but it doesnt do anything else)

import sys
s = sys.argv[0]

this says get the string that is stored at

index 0 in the list sys.argv and assign it
to the variable s

Numbers
Python defines various types of numbers:

Integer (1234)
Floating point number (12.34)
Octal and hexadecimal number (0177, 0x9gff)
Complex number (3.0+4.1j)

You will likely only need the first two.

Conversions
>>> 6/2
3
>>> 3/4
0
>>> 3.0/4.0
0.75
>>> 3/4.0
0.75
>>> 3*4
12
>>> 3*4.0
12.0

truncated rather than

rounded

The result of a mathematical

operation on two numbers of
the same type is a number of
that type.
The result of an operation on
two numbers of different
types is a number of the more
complex type.
integer float

Formatting numbers
The % operator formats a number.
The syntax is <format> % <number>
>>> %f % 3
3.000000
>>> %.2f % 3
3.00
>>> %5.2f % 3
3.00

Formatting codes

%d = integer (d as in digit)
%f = float value - decimal (floating point) number
%e = scientific notation
%g = easily readable notation (i.e., use decimal
notation unless there are too many zeroes, then
switch to scientific notation)

More complex formats

%[flags][width][.precision][code]
Total width
of output

Left justify (-)

Include numeric sign (+)
Fill in with zeroes (0)

Number of
digits after
decimal

d, f, e, g

Examples
>>> x = 7718
>>> %d % x
7718
>>> %-6d % x
7718
>>> %06d % x
007718
>>> x = 1.23456789
>>> %d % x
1
>>> %f % x
1.234568
>>> %e % x
1.234568e+00
>>> %g % x
1.23457
>>> %g % (x * 10000000)
1.23457e+07

Read as use the preceding code

to format the following number

Dont worry if this all looks like

Greek you can figure out how
to do these when you need
them in your programs.
.

string basics
Basic string operations:
S = "AATTGG"
S1 + S2
S*3
S[i]
S[x:y]
len(S)
int(S)
float(S)
len(S[x:y])

# assignment - or use single quotes ' '

# concatenate two strings
# repeat string S 3 times
# get character at position 'i'
# get a substring from x to y (not including y)
# get length of string
# turn a string into an integer
# turn a string into a floating point decimal number
# the length of s[x:y] is always y - x

Methods:
S.upper()
# convert S to all upper case, return the new string
S.lower()
# convert S to all lower case, return the new string
S.count(substring)
# return number of times substring appears in S
S.replace(old,new)
# replace all appearances of old with new, return the new string
S.find(substring)
# return index of first appearance of substring in S
S.find(substring, index)
# same as previous but starts search at index in S
S.startswith(substring)
# return True or False
S.endswith(substring)
# return True of False
Printing:
print var1,var2,var3
print "text",var1,"text"

# print multiple variables with space between each

# print a combination of explicit text and variables

list basics
Basic list operations:
L = ['dna','rna','protein']
# list assignment
L2 = [1,2,'dogma',L]
# list can hold different object types
L2[2] = 'central'
# change an element (mutable)
L2[0:2] = 'ACGT'
# replace a slice
del L[0:1] = 'nucs'
# delete a slice
L2 + L
# concatenate
L2*3
# repeat list
L[x:y]
# get a slice of a list
len(L)
# length of list
''.join(L)
# convert a list to a string (a string function that acts on lists)
S.split(x)
# convert string to list- x delimited
list(S)
# convert string to list - explode
list(T)
# converts a tuple to list

Methods:
L.append(x)
L.extend(x)
L.count(x)
L.index(x)
L.insert(i,x)
L.remove(x)
L.pop(i)
L.reverse()
L.sort()

# add to the end

# append each element from x to list
# count the occurrences of x
# get element position of first occurrence of x
# insert element x at position i
# delete first occurrence of x
# extract (and delete) element at position i
# reverse list in place
# sort list in place

dict basics
D = {'dna':'T','rna':'U'}
D = {}
D.keys()
D.values()
D['dna']
D['dna'] = 'T'
del D['dna']
D.pop('dna')
'dna' in D

# dictionary literal assignment

# make an empty dictionary
# get the keys as a list
# get the values as a list
# get a value based on key
# set a key:value pair
# delete a key:value pair
# remove key:value (and return value)
# True if key 'dna' is found in D, else False

The keys must be immutable objects (e.g. string, int, tuple).

The values can be anything (including a list or another dictionary).

The order of elements in the list returned by D.keys() or D.values()
is arbitrary (effectively random).

File reading and writing

The open() command returns a file object:
<file_object> = open(<filename>, <access type>)
Access types:

'r' = read
'w' = write
'a' = append

myFile = open("data.txt", "r") open for reading

myFile = open("new_data.txt", "w") open for writing
myString = myFile.read() read the entire text as a string
myStringList = myFile.readlines() read all the lines as a list of strings
myString = myFile.readline() read the next line as a string
myFile.write(foo) write a string (does not append a newline)
myFile.close() always close a file after done

if elif - else
if <test1>:
<block1>
elif <test2>:
<block2>
elif <test3>:
<block3>
else:
<block4>
Only one of the blocks is ever executed.
A block is all code with the same indentation.

Comparison operators
Boolean: and, or, not
Numeric: < , > , ==, !=, >=, <=
String: in, not in
<
>
==
!=
<=
>=

is
is
is
is
is
is

less than
greater than
equal to
NOT equal to
less than or equal to
greater than or equal to

for loops
for <target> in <object>

object can be a list, a string, a tuple

for letter in Constinople

for myString in myList

(where myList is a list of strings)

continue

skip the rest of the loop and start at the top again

break

quit the loop immediately

As usual, all the commands with the same indentation are run as a code block.
for integer in range(12)

range simply returns a list of integers

range([start,] stop [,step])

Loops can be nested or have other complex code blocks inside them.

Examples of for loops

for base in sequence:
<do something with each base>
for sequence in database:
<do something with each sequence>
for base in ["a","c","g","t"]:
<do something with each base>

for index in range(5,200):

<do something with each index.

while loops
Similar to a for loop
while (conditional test):
<statement1>
<statement2>
. . .
<last statement>
While something is True keep running the loop, exit as
soon as the test is False.
Any expression that evaluates True/False can be used
for the conditional test.

Examples of while loops

while (error > 0.05):
<do something that will reduce error>

while (score > 0):

<traceback through a DP matrix, each
time setting the current score>

Time efficiency
Rough order of speed for common operations:
reading/writing files - very slow
going through a list serially for matching elements - slow
accessing a list (or string) element by index - fast
accessing a dictionary value by key - fast
File reading - sometimes you only need to look through a file until you find
something. In this case, read lines until you have what you need then close
the file.
Dictionaries can be used in various clever ways to save time.
Do simple profiling to see what part of your code is slowest (for example,
invoke time.time() twice, once before and once after a code block).
Future - beginning Python is kept simple by hiding a lot of complex things
from you - dig in deeper to understand what takes more time (and memory).

Memory efficiency
File reading - often you don't need to save the entire contents of a file into
memory. Consider whether you can discard some of the information.
If your program generates many copies of a long string, consider making a
dictionary entry with the string as the value (you only need to store it once).
If you are working with a long string and you want to access many segments
of it, do NOT save each segment as a string - use string indexing to get
each segment as you need it.
Future - instead of using Python lists, consider using classes in the Python
array module to store long sequences, etc.